Question: I: R: R: R: Probe-level analysis of exon arrays using xps

0

Lavorgna Giovanni •

**80**wrote:Dear Christian,
thanks for your answer. Sorry for not being clear in my previous
massage. I'll try to clarify things a little bit more.
The following script running in a R session ( xps_1.12.1 + root
5.27/04) crashes after finishing the rma step, i.e., it completes the
line:
rma.ps.core <- rma(data.mix.exon, "MixExonRMAcorePS_prostate_CPU2",
filedir=libdir, tmpdir="", background="antigenomic", normalize=TRUE,
option="probeset", exonlevel="affx+core")
producing both the correct root and text files, then hangs and gets
killed by the system after memory consumption gets over 90%.
===========================================
R script
library (xps)
### define directories:
# directory containing Affymetrix library files
libdir <- "/home/lavorgna/"
# directory containing Affymetrix annotation files
anndir <- "/home/lavorgna/"
# directory to store ROOT scheme files
scmdir <- "/home/lavorgna/"
datdir <- "/home/lavorgna/"
tmpdir <- "/home/lavorgna/"
### first, load ROOT scheme file and ROOT data file
scheme.exon <- root.scheme(file.path(scmdir, "HuEx-1_0-st-v2.root"))
data.mix.exon <- root.data(scheme.exon, file.path(datdir,
"tmpdt_prostate_whole_cel_20110829_181922.root"))
### RMA for probesets. To execute the dabg step, comment out next
line.
rma.ps.core <- rma(data.mix.exon, "MixExonRMAcorePS_prostate_CPU2",
filedir=libdir, tmpdir="", background="antigenomic", normalize=TRUE,
option="probeset", exonlevel="affx+core")
## DABG detection call
dabg.ps <- dabg.call(data.mix.exon, "MixDABGcorePS_prostate_CPU2",
filedir=libdir, option="probeset", exonlevel="affx+core")
===================================
However, if I comment out the rma line and I run the script under the
same conditions under a new R session I can get the dabg root file and
the text files (at least partially), though the script finally crashes
without a normal exit.
I enclose both log files and the sessionInfo. Please let me know if
you would like me to provide more information.
Giovanni
====================================
Log file of the script without commented out rna line
Creating new file
</home>...
Opening file </home> in <read> mode...
Opening file
</home> in
<read> mode...
Warning in <tstreamerinfo::compile>: Counter fNClusterRange should not
be skipped from class TTree
Added <185> trees to PreprocesSet.
Preprocessing data using method <preprocess>...
Background correcting raw data...
setting selector mask for typepm <9276>
calculating background for <gsm526134_yx_exon1_pca0001.cel>...
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calculating background for <gsm526276_yx_exon1_pca0206.cel>...
background statistics:
5468682 cells with minimal intensity 0
6 cells with maximal intensity 103.452
calculating background for <gsm526277_yx_exon1_pca0207.cel>...
background statistics:
5468682 cells with minimal intensity 0
336 cells with maximal intensity 77.3287
calculating background for <gsm526278_yx_exon1_pca0208.cel>...
background statistics:
5468682 cells with minimal intensity 0
37 cells with maximal intensity 363.026
calculating background for <gsm526279_yx_pca0209_huex_1.cel>...
background statistics:
5468682 cells with minimal intensity 0
1675 cells with maximal intensity 32.6269
calculating background for <gsm526280_yx_pca0210_huex_1.cel>...
background statistics:
5468682 cells with minimal intensity 0
729505 cells with maximal intensity 37.7769
calculating background for <gsm526281_yx_exon1_pca0211.cel>...
background statistics:
5468682 cells with minimal intensity 0
3135 cells with maximal intensity 63.6604
calculating background for <gsm526282_yx_exon1_pca0213.cel>...
background statistics:
5468682 cells with minimal intensity 0
6 cells with maximal intensity 116.958
calculating background for <gsm526283_yx_pca0215_huex_1.cel>...
background statistics:
5468682 cells with minimal intensity 0
20 cells with maximal intensity 53.4464
calculating background for <gsm526284_yx_exon1_du145.cel>...
background statistics:
5468682 cells with minimal intensity 0
53 cells with maximal intensity 63.8819
calculating background for <gsm526285_yx_exon1_lncap.cel>...
background statistics:
5468682 cells with minimal intensity 0
10264 cells with maximal intensity 89.5586
calculating background for <gsm526286_yx_exon1_lncap104r.cel>...
background statistics:
5468682 cells with minimal intensity 0
59 cells with maximal intensity 42.3791
calculating background for <gsm526287_yx_exon1_lncap104s.cel>...
background statistics:
5468682 cells with minimal intensity 0
15175 cells with maximal intensity 38.1814
calculating background for <gsm526288_yx_exon1_pc3.cel>...
background statistics:
5468682 cells with minimal intensity 0
51972 cells with maximal intensity 78.1985
calculating background for <gsm526289_yx_exon1_vcap.cel>...
background statistics:
5468682 cells with minimal intensity 0
4 cells with maximal intensity 97.8876
calculating background for <gsm526290_yx_exon1_pan0095.cel>...
background statistics:
5468682 cells with minimal intensity 0
165 cells with maximal intensity 40.4709
calculating background for <gsm526291_yx_exon1_pan0107.cel>...
background statistics:
5468682 cells with minimal intensity 0
274 cells with maximal intensity 65.3504
calculating background for <gsm526292_yx_exon1_pan0109.cel>...
background statistics:
5468682 cells with minimal intensity 0
3 cells with maximal intensity 75.9984
calculating background for <gsm526293_yx_exon1_pan0110.cel>...
background statistics:
5468682 cells with minimal intensity 0
3856 cells with maximal intensity 65.984
calculating background for <gsm526294_yx_exon1_pan0112.cel>...
background statistics:
5468682 cells with minimal intensity 0
280597 cells with maximal intensity 69.4771
calculating background for <gsm526295_yx_exon1_pan0113.cel>...
background statistics:
5468682 cells with minimal intensity 0
1 cells with maximal intensity 55.8045
calculating background for <gsm526296_yx_exon1_pan0114.cel>...
background statistics:
5468682 cells with minimal intensity 0
20107 cells with maximal intensity 61.2959
calculating background for <gsm526297_yx_exon1_pan0115.cel>...
background statistics:
5468682 cells with minimal intensity 0
209 cells with maximal intensity 61.0952
calculating background for <gsm526298_yx_exon1_pan0117.cel>...
background statistics:
5468682 cells with minimal intensity 0
3 cells with maximal intensity 65.0484
calculating background for <gsm526299_yx_exon1_pan0120.cel>...
background statistics:
5468682 cells with minimal intensity 0
41327 cells with maximal intensity 78.2326
calculating background for <gsm526300_yx_exon1_pan0122.cel>...
background statistics:
5468682 cells with minimal intensity 0
1153 cells with maximal intensity 47.9351
calculating background for <gsm526301_yx_exon1_pan0125.cel>...
background statistics:
5468682 cells with minimal intensity 0
122 cells with maximal intensity 46.1842
calculating background for <gsm526302_yx_exon1_pan0127.cel>...
background statistics:
5468682 cells with minimal intensity 0
2 cells with maximal intensity 59.3748
calculating background for <gsm526303_yx_exon1_pan0128.cel>...
background statistics:
5468682 cells with minimal intensity 0
3 cells with maximal intensity 75.8692
calculating background for <gsm526304_yx_exon1_pan0129.cel>...
background statistics:
5468682 cells with minimal intensity 0
1395 cells with maximal intensity 84.0785
calculating background for <gsm526305_yx_exon1_pan0134.cel>...
background statistics:
5468682 cells with minimal intensity 0
243 cells with maximal intensity 84.6977
calculating background for <gsm526306_yx_exon1_pan0135.cel>...
background statistics:
5468682 cells with minimal intensity 0
18046 cells with maximal intensity 62.9549
calculating background for <gsm526307_yx_exon1_pan0136.cel>...
background statistics:
5468682 cells with minimal intensity 0
2850 cells with maximal intensity 35.9795
calculating background for <gsm526308_yx_exon1_pan0144.cel>...
background statistics:
5468682 cells with minimal intensity 0
1387 cells with maximal intensity 43.2994
calculating background for <gsm526309_yx_exon1_pan0147.cel>...
background statistics:
5468682 cells with minimal intensity 0
1027 cells with maximal intensity 40.5652
calculating background for <gsm526310_yx_exon1_pan0151.cel>...
background statistics:
5468682 cells with minimal intensity 0
21307 cells with maximal intensity 54.4608
calculating background for <gsm526311_yx_exon1_pan0157.cel>...
background statistics:
5468682 cells with minimal intensity 0
2712 cells with maximal intensity 42.3063
calculating background for <gsm526312_yx_exon1_pan0162.cel>...
background statistics:
5468682 cells with minimal intensity 0
282 cells with maximal intensity 52.5074
calculating background for <gsm526313_yx_exon1_pan0164.cel>...
background statistics:
5468682 cells with minimal intensity 0
40978 cells with maximal intensity 55.2205
calculating background for <gsm526314_yx_exon1_pan0167.cel>...
background statistics:
5468682 cells with minimal intensity 0
5 cells with maximal intensity 50.8994
calculating background for <gsm526315_yx_exon1_pan0169.cel>...
background statistics:
5468682 cells with minimal intensity 0
186 cells with maximal intensity 43.2757
calculating background for <gsm526316_yx_exon1_pan0171.cel>...
background statistics:
5468682 cells with minimal intensity 0
11622 cells with maximal intensity 42.5357
calculating background for <gsm526317_yx_exon1_pan0172.cel>...
background statistics:
5468682 cells with minimal intensity 0
277133 cells with maximal intensity 61.8141
calculating background for <gsm526318_yx_exon1_pan0174.cel>...
background statistics:
5468682 cells with minimal intensity 0
5 cells with maximal intensity 61.0677
Normalizing raw data...
normalizing data using method <quantile>...
setting selector mask for typepm <9276>
finished filling <185> arrays. 0174>...
computing common mean...
finished filling <185> trees. PAN0174.cqu>...
Converting raw data to expression levels...
summarizing with <medianpolish>...
setting selector mask for typepm <9276>
setting selector mask for typepm <9276>
calculating expression for <284836> of <1432143>
units...Finished.
expression statistics for GSM526134_YX_Exon1_PCA0001.mdp:
minimal expression level is <9.05221>
maximal expression level is <36667.3>
expression statistics for GSM526135_YX_Exon1_PCA0002.mdp:
minimal expression level is <9.00212>
maximal expression level is <29771>
expression statistics for GSM526136_YX_Exon1_PCA0003.mdp:
minimal expression level is <8.92135>
maximal expression level is <31817.6>
expression statistics for GSM526137_YX_Exon1_PCA0005.mdp:
minimal expression level is <8.81214>
maximal expression level is <31817.6>
expression statistics for GSM526138_YX_Exon1_PCA0007.mdp:
minimal expression level is <8.76413>
maximal expression level is <33863.9>
expression statistics for GSM526139_YX_Exon1_PCA0008.mdp:
minimal expression level is <9.08348>
maximal expression level is <26401.7>
expression statistics for GSM526140_YX_Exon1_PCA0009.mdp:
minimal expression level is <8.88344>
maximal expression level is <42146>
expression statistics for GSM526141_YX_Exon1_PCA0010.mdp:
minimal expression level is <8.97541>
maximal expression level is <29062.5>
expression statistics for GSM526142_YX_Exon1_PCA0011.mdp:
minimal expression level is <9.03306>
maximal expression level is <29537.4>
expression statistics for GSM526143_YX_Exon1_PCA0012.mdp:
minimal expression level is <8.87733>
maximal expression level is <28120.4>
expression statistics for GSM526144_YX_Exon1_PCA0013.mdp:
minimal expression level is <9.00688>
maximal expression level is <29606.5>
expression statistics for GSM526145_YX_Exon1_PCA0014.mdp:
minimal expression level is <8.84191>
maximal expression level is <28023.9>
expression statistics for GSM526146_YX_Exon1_PCA0015.mdp:
minimal expression level is <8.79881>
maximal expression level is <34946.1>
expression statistics for GSM526147_YX_Exon1_PCA0017.mdp:
minimal expression level is <8.57668>
maximal expression level is <33863.9>
expression statistics for GSM526148_YX_Exon1_PCA0018.mdp:
minimal expression level is <9.1399>
maximal expression level is <36667.3>
expression statistics for GSM526149_YX_Exon1_PCA0020.mdp:
minimal expression level is <8.77847>
maximal expression level is <34144.7>
expression statistics for GSM526150_YX_Exon1_PCA0021.mdp:
minimal expression level is <8.97541>
maximal expression level is <28078.5>
expression statistics for GSM526151_YX_Exon1_PCA0022.mdp:
minimal expression level is <8.88741>
maximal expression level is <25993>
expression statistics for GSM526152_YX_Exon1_PCA0024.mdp:
minimal expression level is <8.83685>
maximal expression level is <29537.4>
expression statistics for GSM526153_YX_Exon1_PCA0025.mdp:
minimal expression level is <8.88344>
maximal expression level is <31817.6>
expression statistics for GSM526154_YX_Exon1_PCA0026.mdp:
minimal expression level is <8.91752>
maximal expression level is <26036.6>
expression statistics for GSM526155_YX_Exon1_PCA0027.mdp:
minimal expression level is <8.76413>
maximal expression level is <44919.8>
expression statistics for GSM526156_YX_Exon1_PCA0028.mdp:
minimal expression level is <8.91752>
maximal expression level is <28537.3>
expression statistics for GSM526157_YX_Exon1_PCA0029.mdp:
minimal expression level is <8.76413>
maximal expression level is <25067.5>
expression statistics for GSM526158_YX_Exon1_PCA0030.mdp:
minimal expression level is <9.0581>
maximal expression level is <29540.8>
expression statistics for GSM526159_YX_Exon1_PCA0031.mdp:
minimal expression level is <8.74241>
maximal expression level is <36667.3>
expression statistics for GSM526160_YX_Exon1_PCA0032.mdp:
minimal expression level is <8.95135>
maximal expression level is <29555.2>
expression statistics for GSM526161_YX_Exon1_PCA0033.mdp:
minimal expression level is <8.96212>
maximal expression level is <44919.8>
expression statistics for GSM526162_YX_Exon1_PCA0034.mdp:
minimal expression level is <9.00872>
maximal expression level is <33863.9>
expression statistics for GSM526163_YX_Exon1_PCA0035.mdp:
minimal expression level is <9.18124>
maximal expression level is <31817.6>
expression statistics for GSM526164_YX_Exon1_PCA0036.mdp:
minimal expression level is <8.75336>
maximal expression level is <36667.3>
expression statistics for GSM526165_YX_Exon1_PCA0037.mdp:
minimal expression level is <9.06177>
maximal expression level is <28993.6>
expression statistics for GSM526166_YX_PCA0038_HuEx_1.mdp:
minimal expression level is <8.90996>
maximal expression level is <32252.6>
expression statistics for GSM526167_YX_Exon1_PCA0040.mdp:
minimal expression level is <8.90996>
maximal expression level is <25473.2>
expression statistics for GSM526168_YX_Exon1_PCA0050.mdp:
minimal expression level is <8.74241>
maximal expression level is <31817.6>
expression statistics for GSM526169_YX_Exon1_PCA0052.mdp:
minimal expression level is <9.02444>
maximal expression level is <36667.3>
expression statistics for GSM526170_YX_Exon1_PCA0054.mdp:
minimal expression level is <8.57668>
maximal expression level is <30444.7>
expression statistics for GSM526171_YX_Exon1_PCA0056.mdp:
minimal expression level is <8.81609>
maximal expression level is <26573.8>
expression statistics for GSM526172_YX_Exon1_PCA0057.mdp:
minimal expression level is <8.94652>
maximal expression level is <36667.3>
expression statistics for GSM526173_YX_PCA0058_HuEx_1.mdp:
minimal expression level is <8.78547>
maximal expression level is <59315.2>
expression statistics for GSM526174_YX_Exon1_PCA0062.mdp:
minimal expression level is <8.68593>
maximal expression level is <44919.8>
expression statistics for GSM526175_YX_Exon1_PCA0063.mdp:
minimal expression level is <8.86881>
maximal expression level is <29537.4>
expression statistics for GSM526176_YX_Exon1_PCA0064.mdp:
minimal expression level is <8.77847>
maximal expression level is <40191.3>
expression statistics for GSM526177_YX_Exon1_PCA0065.mdp:
minimal expression level is <8.98222>
maximal expression level is <44919.8>
expression statistics for GSM526178_YX_Exon1_PCA0066.mdp:
minimal expression level is <8.74241>
maximal expression level is <33863.9>
expression statistics for GSM526179_YX_Exon1_PCA0068.mdp:
minimal expression level is <9.00929>
maximal expression level is <36667.3>
expression statistics for GSM526180_YX_Exon1_PCA0073.mdp:
minimal expression level is <8.79213>
maximal expression level is <36667.3>
expression statistics for GSM526181_YX_Exon1_PCA0074.mdp:
minimal expression level is <8.85977>
maximal expression level is <24177>
expression statistics for GSM526182_YX_Exon1_PCA0075.mdp:
minimal expression level is <8.68593>
maximal expression level is <33863.9>
expression statistics for GSM526183_YX_Exon1_PCA0077.mdp:
minimal expression level is <8.76953>
maximal expression level is <24890.6>
expression statistics for GSM526184_YX_Exon1_PCA0080.mdp:
minimal expression level is <8.85977>
maximal expression level is <27437>
expression statistics for GSM526185_YX_Exon1_PCA0081.mdp:
minimal expression level is <8.90329>
maximal expression level is <50917.6>
expression statistics for GSM526186_YX_Exon1_PCA0082.mdp:
minimal expression level is <8.88444>
maximal expression level is <28023.9>
expression statistics for GSM526187_YX_Exon1_PCA0083.mdp:
minimal expression level is <8.93063>
maximal expression level is <29537.4>
expression statistics for GSM526188_YX_PCA0084_HuEx_1.mdp:
minimal expression level is <9.03184>
maximal expression level is <28770.7>
expression statistics for GSM526189_YX_Exon1_PCA0086.mdp:
minimal expression level is <8.63087>
maximal expression level is <28023.9>
expression statistics for GSM526190_YX_Exon1_PCA0087.mdp:
minimal expression level is <9.13538>
maximal expression level is <25954.2>
expression statistics for GSM526191_YX_Exon1_PCA0089.mdp:
minimal expression level is <8.88444>
maximal expression level is <25954.2>
expression statistics for GSM526192_YX_Exon1_PCA0090.mdp:
minimal expression level is <8.99672>
maximal expression level is <26573.8>
expression statistics for GSM526193_YX_Exon1_PCA0092.mdp:
minimal expression level is <9.07449>
maximal expression level is <24172.9>
expression statistics for GSM526194_YX_Exon1_PCA0093.mdp:
minimal expression level is <8.84756>
maximal expression level is <25243.7>
expression statistics for GSM526195_YX_Exon1_PCA0094.mdp:
minimal expression level is <8.76953>
maximal expression level is <26708.8>
expression statistics for GSM526196_YX_Exon1_PCA0095.mdp:
minimal expression level is <8.87733>
maximal expression level is <28023.9>
expression statistics for GSM526197_YX_Exon1_PCA0096.mdp:
minimal expression level is <9.0762>
maximal expression level is <26981.1>
expression statistics for GSM526198_YX_Exon1_PCA0097.mdp:
minimal expression level is <8.79213>
maximal expression level is <26981.1>
expression statistics for GSM526199_YX_Exon1_PCA0099.mdp:
minimal expression level is <8.75336>
maximal expression level is <30620.2>
expression statistics for GSM526200_YX_Exon1_PCA0100.mdp:
minimal expression level is <8.80505>
maximal expression level is <24110.8>
expression statistics for GSM526201_YX_Exon1_PCA0101.mdp:
minimal expression level is <8.99545>
maximal expression level is <33863.9>
expression statistics for GSM526202_YX_Exon1_PCA0103.mdp:
minimal expression level is <9.02798>
maximal expression level is <33863.9>
expression statistics for GSM526203_YX_Exon1_PCA0104.mdp:
minimal expression level is <8.94305>
maximal expression level is <22436.6>
expression statistics for GSM526204_YX_Exon1_PCA0105.mdp:
minimal expression level is <8.93498>
maximal expression level is <28023.9>
expression statistics for GSM526205_YX_Exon1_PCA0107.mdp:
minimal expression level is <8.90128>
maximal expression level is <36667.3>
expression statistics for GSM526206_YX_Exon1_PCA0108.mdp:
minimal expression level is <9.15861>
maximal expression level is <27171.1>
expression statistics for GSM526207_YX_Exon1_PCA0109.mdp:
minimal expression level is <9.09492>
maximal expression level is <31817.6>
expression statistics for GSM526208_YX_Exon1_PCA0110.mdp:
minimal expression level is <8.66385>
maximal expression level is <25954.2>
expression statistics for GSM526209_YX_Exon1_PCA0111.mdp:
minimal expression level is <8.74241>
maximal expression level is <24825.7>
expression statistics for GSM526210_YX_Exon1_PCA0112.mdp:
minimal expression level is <8.57668>
maximal expression level is <20685>
expression statistics for GSM526211_YX_Exon1_PCA0113.mdp:
minimal expression level is <8.79213>
maximal expression level is <28219.4>
expression statistics for GSM526212_YX_Exon1_PCA0114.mdp:
minimal expression level is <8.83195>
maximal expression level is <25704.8>
expression statistics for GSM526213_YX_Exon1_PCA0115.mdp:
minimal expression level is <8.74241>
maximal expression level is <25473.2>
expression statistics for GSM526214_YX_Exon1_PCA0117.mdp:
minimal expression level is <8.57668>
maximal expression level is <29537.4>
expression statistics for GSM526215_YX_Exon1_PCA0118.mdp:
minimal expression level is <8.97826>
maximal expression level is <25704.8>
expression statistics for GSM526216_YX_Exon1_PCA0119.mdp:
minimal expression level is <8.88067>
maximal expression level is <25473.2>
expression statistics for GSM526217_YX_Exon1_PCA0120.mdp:
minimal expression level is <8.74241>
maximal expression level is <27437>
expression statistics for GSM526218_YX_Exon1_PCA0122.mdp:
minimal expression level is <9.03533>
maximal expression level is <29537.4>
expression statistics for GSM526219_YX_Exon1_PCA0123.mdp:
minimal expression level is <9.11065>
maximal expression level is <29537.4>
expression statistics for GSM526220_YX_Exon1_PCA0124.mdp:
minimal expression level is <8.77847>
maximal expression level is <36667.3>
expression statistics for GSM526221_YX_Exon1_PCA0125.mdp:
minimal expression level is <8.88444>
maximal expression level is <40191.3>
expression statistics for GSM526222_YX_Exon1_PCA0126.mdp:
minimal expression level is <8.57668>
maximal expression level is <24653.2>
expression statistics for GSM526223_YX_Exon1_PCA0127.mdp:
minimal expression level is <8.97136>
maximal expression level is <23102.7>
expression statistics for GSM526224_YX_Exon1_PCA0128.mdp:
minimal expression level is <8.78547>
maximal expression level is <50917.6>
expression statistics for GSM526225_YX_Exon1_PCA0129.mdp:
minimal expression level is <8.77847>
maximal expression level is <25116.7>
expression statistics for GSM526226_YX_Exon1_PCA0130.mdp:
minimal expression level is <9.09968>
maximal expression level is <59315.2>
expression statistics for GSM526227_YX_Exon1_PCA0132.mdp:
minimal expression level is <8.83685>
maximal expression level is <36667.3>
expression statistics for GSM526228_YX_Exon1_PCA0133.mdp:
minimal expression level is <8.70688>
maximal expression level is <28023.9>
expression statistics for GSM526229_YX_Exon1_PCA0134.mdp:
minimal expression level is <8.83685>
maximal expression level is <22376.8>
expression statistics for GSM526230_YX_Exon1_PCA0135.mdp:
minimal expression level is <8.96716>
maximal expression level is <31817.6>
expression statistics for GSM526231_YX_Exon1_PCA0136.mdp:
minimal expression level is <8.80505>
maximal expression level is <27437>
expression statistics for GSM526232_YX_Exon1_PCA0141.mdp:
minimal expression level is <8.68593>
maximal expression level is <33863.9>
expression statistics for GSM526233_YX_Exon1_PCA0144.mdp:
minimal expression level is <9.08348>
maximal expression level is <23809.9>
expression statistics for GSM526234_YX_Exon1_PCA0145.mdp:
minimal expression level is <9.10392>
maximal expression level is <44919.8>
expression statistics for GSM526235_YX_Exon1_PCA0146.mdp:
minimal expression level is <8.82445>
maximal expression level is <28537.3>
expression statistics for GSM526236_YX_Exon1_PCA0147.mdp:
minimal expression level is <8.81609>
maximal expression level is <59315.2>
expression statistics for GSM526237_YX_Exon1_PCA0149.mdp:
minimal expression level is <8.99545>
maximal expression level is <31817.6>
expression statistics for GSM526238_YX_PCA0150_HuEx_1.mdp:
minimal expression level is <8.88344>
maximal expression level is <25969.1>
expression statistics for GSM526239_YX_Exon1_PCA0151.mdp:
minimal expression level is <8.89413>
maximal expression level is <59315.2>
expression statistics for GSM526240_YX_Exon1_PCA0155.mdp:
minimal expression level is <9.04111>
maximal expression level is <32387.4>
expression statistics for GSM526241_YX_Exon1_PCA0156.mdp:
minimal expression level is <9.00007>
maximal expression level is <36667.3>
expression statistics for GSM526242_YX_Exon1_PCA0157.mdp:
minimal expression level is <8.94246>
maximal expression level is <28709.2>
expression statistics for GSM526243_YX_Exon1_PCA0158.mdp:
minimal expression level is <9.08814>
maximal expression level is <44919.8>
expression statistics for GSM526244_YX_Exon1_PCA0159.mdp:
minimal expression level is <8.79881>
maximal expression level is <26573.8>
expression statistics for GSM526245_YX_Exon1_PCA0160.mdp:
minimal expression level is <9.06629>
maximal expression level is <36667.3>
expression statistics for GSM526246_YX_Exon1_PCA0161.mdp:
minimal expression level is <8.77847>
maximal expression level is <30534.4>
expression statistics for GSM526247_YX_Exon1_PCA0162.mdp:
minimal expression level is <8.91218>
maximal expression level is <34144.7>
expression statistics for GSM526248_YX_Exon1_PCA0163.mdp:
minimal expression level is <8.72497>
maximal expression level is <44919.8>
expression statistics for GSM526249_YX_Exon1_PCA0164.mdp:
minimal expression level is <8.63087>
maximal expression level is <31817.6>
expression statistics for GSM526250_YX_Exon1_PCA0165.mdp:
minimal expression level is <8.97136>
maximal expression level is <28986.5>
expression statistics for GSM526251_YX_Exon1_PCA0167.mdp:
minimal expression level is <9.03533>
maximal expression level is <27524.6>
expression statistics for GSM526252_YX_Exon1_PCA0168.mdp:
minimal expression level is <8.84756>
maximal expression level is <31817.6>
expression statistics for GSM526253_YX_Exon1_PCA0169.mdp:
minimal expression level is <9.04919>
maximal expression level is <24653.2>
expression statistics for GSM526254_YX_Exon1_PCA0170.mdp:
minimal expression level is <8.75336>
maximal expression level is <40191.3>
expression statistics for GSM526255_YX_Exon1_PCA0171.mdp:
minimal expression level is <8.88741>
maximal expression level is <36667.3>
expression statistics for GSM526256_YX_Exon1_PCA0172.mdp:
minimal expression level is <9.00688>
maximal expression level is <50917.6>
expression statistics for GSM526257_YX_Exon1_PCA0173.mdp:
minimal expression level is <8.96836>
maximal expression level is <40191.3>
expression statistics for GSM526258_YX_Exon1_PCA0174.mdp:
minimal expression level is <8.86881>
maximal expression level is <31817.6>
expression statistics for GSM526259_YX_Exon1_PCA0175.mdp:
minimal expression level is <8.89144>
maximal expression level is <36667.3>
expression statistics for GSM526260_YX_Exon1_PCA0176.mdp:
minimal expression level is <8.63087>
maximal expression level is <24374.3>
expression statistics for GSM526261_YX_Exon1_PCA0178.mdp:
minimal expression level is <8.88344>
maximal expression level is <40191.3>
expression statistics for GSM526262_YX_Exon1_PCA0179.mdp:
minimal expression level is <8.57668>
maximal expression level is <21759.3>
expression statistics for GSM526263_YX_Exon1_PCA0180.mdp:
minimal expression level is <8.85427>
maximal expression level is <31817.6>
expression statistics for GSM526264_YX_Exon1_PCA0181.mdp:
minimal expression level is <9.02276>
maximal expression level is <29537.4>
expression statistics for GSM526265_YX_Exon1_PCA0182.mdp:
minimal expression level is <8.99243>
maximal expression level is <30227.2>
expression statistics for GSM526266_YX_Exon1_PCA0184.mdp:
minimal expression level is <8.90996>
maximal expression level is <25469.1>
expression statistics for GSM526267_YX_Exon1_PCA0187.mdp:
minimal expression level is <8.85427>
maximal expression level is <44919.8>
expression statistics for GSM526268_YX_Exon1_PCA0188.mdp:
minimal expression level is <8.93498>
maximal expression level is <27210.9>
expression statistics for GSM526269_YX_Exon1_PCA0189.mdp:
minimal expression level is <8.68436>
maximal expression level is <31817.6>
expression statistics for GSM526270_YX_Exon1_PCA0190.mdp:
minimal expression level is <8.86881>
maximal expression level is <23966>
expression statistics for GSM526271_YX_Exon1_PCA0193.mdp:
minimal expression level is <8.70688>
maximal expression level is <26981.1>
expression statistics for GSM526272_YX_Exon1_PCA0194.mdp:
minimal expression level is <8.88344>
maximal expression level is <25067.5>
expression statistics for GSM526273_YX_Exon1_PCA0199.mdp:
minimal expression level is <8.78547>
maximal expression level is <30115.4>
expression statistics for GSM526274_YX_Exon1_PCA0200.mdp:
minimal expression level is <8.9936>
maximal expression level is <50917.6>
expression statistics for GSM526275_YX_Exon1_PCA0201.mdp:
minimal expression level is <8.75336>
maximal expression level is <36667.3>
expression statistics for GSM526276_YX_Exon1_PCA0206.mdp:
minimal expression level is <8.81214>
maximal expression level is <29537.4>
expression statistics for GSM526277_YX_Exon1_PCA0207.mdp:
minimal expression level is <8.85152>
maximal expression level is <28023.9>
expression statistics for GSM526278_YX_Exon1_PCA0208.mdp:
minimal expression level is <8.84058>
maximal expression level is <21952.6>
expression statistics for GSM526279_YX_PCA0209_HuEx_1.mdp:
minimal expression level is <8.93498>
maximal expression level is <29636.5>
expression statistics for GSM526280_YX_PCA0210_HuEx_1.mdp:
minimal expression level is <8.84191>
maximal expression level is <26600>
expression statistics for GSM526281_YX_Exon1_PCA0211.mdp:
minimal expression level is <8.66385>
maximal expression level is <27437>
expression statistics for GSM526282_YX_Exon1_PCA0213.mdp:
minimal expression level is <8.86881>
maximal expression level is <25351.8>
expression statistics for GSM526283_YX_PCA0215_HuEx_1.mdp:
minimal expression level is <8.92945>
maximal expression level is <30656.3>
expression statistics for GSM526284_YX_Exon1_DU145.mdp:
minimal expression level is <9.01108>
maximal expression level is <27437>
expression statistics for GSM526285_YX_Exon1_LNCaP.mdp:
minimal expression level is <8.96597>
maximal expression level is <30534.4>
expression statistics for GSM526286_YX_Exon1_LNCaP104R.mdp:
minimal expression level is <9.06295>
maximal expression level is <30534.4>
expression statistics for GSM526287_YX_Exon1_LNCaP104S.mdp:
minimal expression level is <8.81609>
maximal expression level is <40191.3>
expression statistics for GSM526288_YX_Exon1_PC3.mdp:
minimal expression level is <8.68593>
maximal expression level is <50917.6>
expression statistics for GSM526289_YX_Exon1_Vcap.mdp:
minimal expression level is <9.11591>
maximal expression level is <36667.3>
expression statistics for GSM526290_YX_Exon1_PAN0095.mdp:
minimal expression level is <8.79213>
maximal expression level is <31817.6>
expression statistics for GSM526291_YX_Exon1_PAN0107.mdp:
minimal expression level is <8.88344>
maximal expression level is <33863.9>
expression statistics for GSM526292_YX_Exon1_PAN0109.mdp:
minimal expression level is <8.88344>
maximal expression level is <31817.6>
expression statistics for GSM526293_YX_Exon1_PAN0110.mdp:
minimal expression level is <8.99946>
maximal expression level is <29537.4>
expression statistics for GSM526294_YX_Exon1_PAN0112.mdp:
minimal expression level is <9.10731>
maximal expression level is <44919.8>
expression statistics for GSM526295_YX_Exon1_PAN0113.mdp:
minimal expression level is <8.80505>
maximal expression level is <50917.6>
expression statistics for GSM526296_YX_Exon1_PAN0114.mdp:
minimal expression level is <8.78547>
maximal expression level is <50917.6>
expression statistics for GSM526297_YX_Exon1_PAN0115.mdp:
minimal expression level is <8.79213>
maximal expression level is <28537.3>
expression statistics for GSM526298_YX_Exon1_PAN0117.mdp:
minimal expression level is <8.97541>
maximal expression level is <25588>
expression statistics for GSM526299_YX_Exon1_PAN0120.mdp:
minimal expression level is <8.99426>
maximal expression level is <26857.9>
expression statistics for GSM526300_YX_Exon1_PAN0122.mdp:
minimal expression level is <8.70688>
maximal expression level is <35299.2>
expression statistics for GSM526301_YX_Exon1_PAN0125.mdp:
minimal expression level is <8.92945>
maximal expression level is <28125.7>
expression statistics for GSM526302_YX_Exon1_PAN0127.mdp:
minimal expression level is <8.92035>
maximal expression level is <31817.6>
expression statistics for GSM526303_YX_Exon1_PAN0128.mdp:
minimal expression level is <8.92035>
maximal expression level is <28537.3>
expression statistics for GSM526304_YX_Exon1_PAN0129.mdp:
minimal expression level is <9.04398>
maximal expression level is <32780.3>
expression statistics for GSM526305_YX_Exon1_PAN0134.mdp:
minimal expression level is <8.83685>
maximal expression level is <33863.9>
expression statistics for GSM526306_YX_Exon1_PAN0135.mdp:
minimal expression level is <8.98845>
maximal expression level is <33969.7>
expression statistics for GSM526307_YX_Exon1_PAN0136.mdp:
minimal expression level is <8.70688>
maximal expression level is <24653.2>
expression statistics for GSM526308_YX_Exon1_PAN0144.mdp:
minimal expression level is <8.77847>
maximal expression level is <25164>
expression statistics for GSM526309_YX_Exon1_PAN0147.mdp:
minimal expression level is <8.94305>
maximal expression level is <29941.6>
expression statistics for GSM526310_YX_Exon1_PAN0151.mdp:
minimal expression level is <8.97541>
maximal expression level is <36667.3>
expression statistics for GSM526311_YX_Exon1_PAN0157.mdp:
minimal expression level is <9.07384>
maximal expression level is <50917.6>
expression statistics for GSM526312_YX_Exon1_PAN0162.mdp:
minimal expression level is <8.93843>
maximal expression level is <50917.6>
expression statistics for GSM526313_YX_Exon1_PAN0164.mdp:
minimal expression level is <8.89144>
maximal expression level is <59315.2>
expression statistics for GSM526314_YX_Exon1_PAN0167.mdp:
minimal expression level is <8.74241>
maximal expression level is <28507.9>
expression statistics for GSM526315_YX_Exon1_PAN0169.mdp:
minimal expression level is <8.98845>
maximal expression level is <44919.8>
expression statistics for GSM526316_YX_Exon1_PAN0171.mdp:
minimal expression level is <8.98462>
maximal expression level is <22593.4>
expression statistics for GSM526317_YX_Exon1_PAN0172.mdp:
minimal expression level is <8.74241>
maximal expression level is <28537.3>
expression statistics for GSM526318_YX_Exon1_PAN0174.mdp:
minimal expression level is <8.76953>
maximal expression level is <33863.9>
preprocessing finished.
Opening file </home> in <read> mode...
Opening file </home> in
<read> mode...
Opening file </home> in
<read> mode...
Exporting data from tree <*> to file
</home>...
Reading entries from <huex-1_0-st-v2.anp> ...Finished
<284836> of <284836> records exported.
Killed
====================================
Log file of the script with commented out rna line
Creating new file </home>...
Opening file </home> in <read> mode...
Opening file
</home> in
<read> mode...
Warning in <tstreamerinfo::compile>: Counter fNClusterRange should not
be skipped from class TTree
Preprocessing data using method <detectcall>...
Calculating detection calls...
setting selector mask for typepm <9276>
setting selector mask for typepm <9276>
calculating present call for <gsm526134_yx_exon1_pca0001.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999966
P: <68.9284> percent units present.
M: <5.34869> percent units marginal.
A: <25.7229> percent units absent.
calculating present call for <gsm526135_yx_exon1_pca0002.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.32086e-36
maximum detection p-value = 1
P: <60.4787> percent units present.
M: <5.26092> percent units marginal.
A: <34.2604> percent units absent.
calculating present call for <gsm526136_yx_exon1_pca0003.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 0.999999
P: <61.0787> percent units present.
M: <6.41738> percent units marginal.
A: <32.504> percent units absent.
calculating present call for <gsm526137_yx_exon1_pca0005.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 1
P: <70.8373> percent units present.
M: <5.31604> percent units marginal.
A: <23.8467> percent units absent.
calculating present call for <gsm526138_yx_exon1_pca0007.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.81285e-36
maximum detection p-value = 1
P: <63.2876> percent units present.
M: <5.4175> percent units marginal.
A: <31.2949> percent units absent.
calculating present call for <gsm526139_yx_exon1_pca0008.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.97754e-36
maximum detection p-value = 1
P: <65.3955> percent units present.
M: <5.35922> percent units marginal.
A: <29.2452> percent units absent.
calculating present call for <gsm526140_yx_exon1_pca0009.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <72.1138> percent units present.
M: <5.55126> percent units marginal.
A: <22.335> percent units absent.
calculating present call for <gsm526141_yx_exon1_pca0010.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <70.7572> percent units present.
M: <4.81646> percent units marginal.
A: <24.4263> percent units absent.
calculating present call for <gsm526142_yx_exon1_pca0011.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999999
P: <64.8987> percent units present.
M: <5.6601> percent units marginal.
A: <29.4412> percent units absent.
calculating present call for <gsm526143_yx_exon1_pca0012.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.00688e-35
maximum detection p-value = 0.999997
P: <65.4752> percent units present.
M: <5.10645> percent units marginal.
A: <29.4183> percent units absent.
calculating present call for <gsm526144_yx_exon1_pca0013.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.2912e-36
maximum detection p-value = 0.99997
P: <69.8637> percent units present.
M: <5.11733> percent units marginal.
A: <25.019> percent units absent.
calculating present call for <gsm526145_yx_exon1_pca0014.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <68.215> percent units present.
M: <4.93758> percent units marginal.
A: <26.8474> percent units absent.
calculating present call for <gsm526146_yx_exon1_pca0015.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <72.1664> percent units present.
M: <4.63881> percent units marginal.
A: <23.1948> percent units absent.
calculating present call for <gsm526147_yx_exon1_pca0017.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <55.2427> percent units present.
M: <6.67858> percent units marginal.
A: <38.0788> percent units absent.
calculating present call for <gsm526148_yx_exon1_pca0018.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 0.999995
P: <62.0413> percent units present.
M: <5.19351> percent units marginal.
A: <32.7652> percent units absent.
calculating present call for <gsm526149_yx_exon1_pca0020.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.54779e-36
maximum detection p-value = 1
P: <70.1502> percent units present.
M: <4.94846> percent units marginal.
A: <24.9013> percent units absent.
calculating present call for <gsm526150_yx_exon1_pca0021.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <63.545> percent units present.
M: <5.62991> percent units marginal.
A: <30.8251> percent units absent.
calculating present call for <gsm526151_yx_exon1_pca0022.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 1
P: <65.517> percent units present.
M: <5.36554> percent units marginal.
A: <29.1175> percent units absent.
calculating present call for <gsm526152_yx_exon1_pca0024.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999998
P: <71.4804> percent units present.
M: <5.69521> percent units marginal.
A: <22.8244> percent units absent.
calculating present call for <gsm526153_yx_exon1_pca0025.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <61.277> percent units present.
M: <5.56496> percent units marginal.
A: <33.158> percent units absent.
calculating present call for <gsm526154_yx_exon1_pca0026.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999968
P: <81.1822> percent units present.
M: <4.52541> percent units marginal.
A: <14.2924> percent units absent.
calculating present call for <gsm526155_yx_exon1_pca0027.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <69.256> percent units present.
M: <5.1728> percent units marginal.
A: <25.5712> percent units absent.
calculating present call for <gsm526156_yx_exon1_pca0028.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.32086e-36
maximum detection p-value = 1
P: <68.6774> percent units present.
M: <4.72798> percent units marginal.
A: <26.5946> percent units absent.
calculating present call for <gsm526157_yx_exon1_pca0029.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.66639e-36
maximum detection p-value = 1
P: <65.2281> percent units present.
M: <5.00604> percent units marginal.
A: <29.7659> percent units absent.
calculating present call for <gsm526158_yx_exon1_pca0030.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.67404e-36
maximum detection p-value = 0.999995
P: <57.6093> percent units present.
M: <5.40838> percent units marginal.
A: <36.9823> percent units absent.
calculating present call for <gsm526159_yx_exon1_pca0031.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.2389e-35
maximum detection p-value = 1
P: <64.1857> percent units present.
M: <6.54552> percent units marginal.
A: <29.2688> percent units absent.
calculating present call for <gsm526160_yx_exon1_pca0032.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.2164e-36
maximum detection p-value = 1
P: <61.4842> percent units present.
M: <5.68222> percent units marginal.
A: <32.8336> percent units absent.
calculating present call for <gsm526161_yx_exon1_pca0033.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 8.47275e-36
maximum detection p-value = 0.999996
P: <58.0418> percent units present.
M: <5.40873> percent units marginal.
A: <36.5495> percent units absent.
calculating present call for <gsm526162_yx_exon1_pca0034.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.2912e-36
maximum detection p-value = 0.999996
P: <67.3623> percent units present.
M: <5.01341> percent units marginal.
A: <27.6243> percent units absent.
calculating present call for <gsm526163_yx_exon1_pca0035.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.10941e-36
maximum detection p-value = 0.999995
P: <66.6471> percent units present.
M: <5.03237> percent units marginal.
A: <28.3205> percent units absent.
calculating present call for <gsm526164_yx_exon1_pca0036.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <67.6024> percent units present.
M: <5.58251> percent units marginal.
A: <26.8151> percent units absent.
calculating present call for <gsm526165_yx_exon1_pca0037.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 1
P: <68.6714> percent units present.
M: <4.72131> percent units marginal.
A: <26.6072> percent units absent.
calculating present call for
<gsm526166_yx_pca0038_huex_1.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <59.5343> percent units present.
M: <5.97853> percent units marginal.
A: <34.4872> percent units absent.
calculating present call for <gsm526167_yx_exon1_pca0040.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.99997
P: <65.5321> percent units present.
M: <6.39421> percent units marginal.
A: <28.0737> percent units absent.
calculating present call for <gsm526168_yx_exon1_pca0050.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <68.0813> percent units present.
M: <6.10246> percent units marginal.
A: <25.8163> percent units absent.
calculating present call for <gsm526169_yx_exon1_pca0052.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 0.999996
P: <65.2877> percent units present.
M: <5.40943> percent units marginal.
A: <29.3028> percent units absent.
calculating present call for <gsm526170_yx_exon1_pca0054.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <75.5171> percent units present.
M: <6.08912> percent units marginal.
A: <18.3937> percent units absent.
calculating present call for <gsm526171_yx_exon1_pca0056.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <74.6749> percent units present.
M: <5.61551> percent units marginal.
A: <19.7096> percent units absent.
calculating present call for <gsm526172_yx_exon1_pca0057.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <72.6962> percent units present.
M: <6.54201> percent units marginal.
A: <20.7618> percent units absent.
calculating present call for
<gsm526173_yx_pca0058_huex_1.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 1
P: <65.2361> percent units present.
M: <5.45366> percent units marginal.
A: <29.3102> percent units absent.
calculating present call for <gsm526174_yx_exon1_pca0062.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <76.6374> percent units present.
M: <5.42066> percent units marginal.
A: <17.9419> percent units absent.
calculating present call for <gsm526175_yx_exon1_pca0063.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.99999
P: <73.9892> percent units present.
M: <5.41083> percent units marginal.
A: <20.5999> percent units absent.
calculating present call for <gsm526176_yx_exon1_pca0064.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999945
P: <74.5661> percent units present.
M: <5.74998> percent units marginal.
A: <19.684> percent units absent.
calculating present call for <gsm526177_yx_exon1_pca0065.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <71.5401> percent units present.
M: <6.17373> percent units marginal.
A: <22.2862> percent units absent.
calculating present call for <gsm526178_yx_exon1_pca0066.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <80.11> percent units present.
M: <4.83928> percent units marginal.
A: <15.0508> percent units absent.
calculating present call for <gsm526179_yx_exon1_pca0068.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999996
P: <64.3051> percent units present.
M: <4.95548> percent units marginal.
A: <30.7394> percent units absent.
calculating present call for <gsm526180_yx_exon1_pca0073.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.2912e-36
maximum detection p-value = 0.999996
P: <72.9866> percent units present.
M: <4.73395> percent units marginal.
A: <22.2795> percent units absent.
calculating present call for <gsm526181_yx_exon1_pca0074.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.65634e-36
maximum detection p-value = 1
P: <62.2449> percent units present.
M: <6.42686> percent units marginal.
A: <31.3282> percent units absent.
calculating present call for <gsm526182_yx_exon1_pca0075.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 1
P: <62.4809> percent units present.
M: <6.01048> percent units marginal.
A: <31.5087> percent units absent.
calculating present call for <gsm526183_yx_exon1_pca0077.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.97754e-36
maximum detection p-value = 1
P: <65.597> percent units present.
M: <6.32926> percent units marginal.
A: <28.0737> percent units absent.
calculating present call for <gsm526184_yx_exon1_pca0080.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 1
P: <74.5197> percent units present.
M: <5.37994> percent units marginal.
A: <20.1003> percent units absent.
calculating present call for <gsm526185_yx_exon1_pca0081.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <65.6041> percent units present.
M: <5.61797> percent units marginal.
A: <28.778> percent units absent.
calculating present call for <gsm526186_yx_exon1_pca0082.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 1
P: <72.2314> percent units present.
M: <5.2876> percent units marginal.
A: <22.481> percent units absent.
calculating present call for <gsm526187_yx_exon1_pca0083.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999946
P: <68.7016> percent units present.
M: <5.61832> percent units marginal.
A: <25.68> percent units absent.
calculating present call for
<gsm526188_yx_pca0084_huex_1.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 1
P: <53.8675> percent units present.
M: <5.61341> percent units marginal.
A: <40.5191> percent units absent.
calculating present call for <gsm526189_yx_exon1_pca0086.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <69.7633> percent units present.
M: <5.26935> percent units marginal.
A: <24.9673> percent units absent.
calculating present call for <gsm526190_yx_exon1_pca0087.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999955
P: <72.9399> percent units present.
M: <5.05484> percent units marginal.
A: <22.0053> percent units absent.
calculating present call for <gsm526191_yx_exon1_pca0089.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.32086e-36
maximum detection p-value = 0.999992
P: <63.1216> percent units present.
M: <6.65997> percent units marginal.
A: <30.2184> percent units absent.
calculating present call for <gsm526192_yx_exon1_pca0090.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999993
P: <70.0126> percent units present.
M: <5.59094> percent units marginal.
A: <24.3965> percent units absent.
calculating present call for <gsm526193_yx_exon1_pca0092.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999975
P: <66.2753> percent units present.
M: <5.43962> percent units marginal.
A: <28.285> percent units absent.
calculating present call for <gsm526194_yx_exon1_pca0093.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 1
P: <73.7663> percent units present.
M: <5.02745> percent units marginal.
A: <21.2062> percent units absent.
calculating present call for <gsm526195_yx_exon1_pca0094.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.98746e-34
maximum detection p-value = 1
P: <65.4861> percent units present.
M: <5.99959> percent units marginal.
A: <28.5143> percent units absent.
calculating present call for <gsm526196_yx_exon1_pca0095.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 1
P: <70.4082> percent units present.
M: <5.3838> percent units marginal.
A: <24.208> percent units absent.
calculating present call for <gsm526197_yx_exon1_pca0096.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.32086e-36
maximum detection p-value = 0.999996
P: <70.4423> percent units present.
M: <5.52072> percent units marginal.
A: <24.037> percent units absent.
calculating present call for <gsm526198_yx_exon1_pca0097.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 8.06623e-36
maximum detection p-value = 0.999979
P: <62.7624> percent units present.
M: <6.14599> percent units marginal.
A: <31.0916> percent units absent.
calculating present call for <gsm526199_yx_exon1_pca0099.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 1
P: <75.9658> percent units present.
M: <4.86104> percent units marginal.
A: <19.1731> percent units absent.
calculating present call for <gsm526200_yx_exon1_pca0100.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <68.3509> percent units present.
M: <5.8395> percent units marginal.
A: <25.8096> percent units absent.
calculating present call for <gsm526201_yx_exon1_pca0101.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999995
P: <72.4189> percent units present.
M: <5.33219> percent units marginal.
A: <22.2489> percent units absent.
calculating present call for <gsm526202_yx_exon1_pca0103.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.05353e-36
maximum detection p-value = 1
P: <73.1691> percent units present.
M: <5.13278> percent units marginal.
A: <21.6981> percent units absent.
calculating present call for <gsm526203_yx_exon1_pca0104.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999991
P: <73.2713> percent units present.
M: <5.0099> percent units marginal.
A: <21.7188> percent units absent.
calculating present call for <gsm526204_yx_exon1_pca0105.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.2912e-36
maximum detection p-value = 0.999953
P: <70.3415> percent units present.
M: <5.31218> percent units marginal.
A: <24.3463> percent units absent.
calculating present call for <gsm526205_yx_exon1_pca0107.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.163e-35
maximum detection p-value = 1
P: <67.5174> percent units present.
M: <5.82686> percent units marginal.
A: <26.6557> percent units absent.
calculating present call for <gsm526206_yx_exon1_pca0108.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999997
P: <65.5335> percent units present.
M: <5.9041> percent units marginal.
A: <28.5624> percent units absent.
calculating present call for <gsm526207_yx_exon1_pca0109.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.99999
P: <70.3907> percent units present.
M: <5.48421> percent units marginal.
A: <24.1251> percent units absent.
calculating present call for <gsm526208_yx_exon1_pca0110.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.65634e-36
maximum detection p-value = 1
P: <55.433> percent units present.
M: <6.69122> percent units marginal.
A: <37.8758> percent units absent.
calculating present call for <gsm526209_yx_exon1_pca0111.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.54779e-36
maximum detection p-value = 1
P: <62.8495> percent units present.
M: <6.34435> percent units marginal.
A: <30.8061> percent units absent.
calculating present call for <gsm526210_yx_exon1_pca0112.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <61.2732> percent units present.
M: <6.07999> percent units marginal.
A: <32.6469> percent units absent.
calculating present call for <gsm526211_yx_exon1_pca0113.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 0.999998
P: <67.6807> percent units present.
M: <6.00486> percent units marginal.
A: <26.3144> percent units absent.
calculating present call for <gsm526212_yx_exon1_pca0114.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.75844e-36
maximum detection p-value = 1
P: <64.9233> percent units present.
M: <6.28326> percent units marginal.
A: <28.7934> percent units absent.
calculating present call for <gsm526213_yx_exon1_pca0115.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 0.999986
P: <68.372> percent units present.
M: <5.96378> percent units marginal.
A: <25.6642> percent units absent.
calculating present call for <gsm526214_yx_exon1_pca0117.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.27644e-36
maximum detection p-value = 1
P: <63.3958> percent units present.
M: <6.30538> percent units marginal.
A: <30.2988> percent units absent.
calculating present call for <gsm526215_yx_exon1_pca0118.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <67.5887> percent units present.
M: <5.93429> percent units marginal.
A: <26.477> percent units absent.
calculating present call for <gsm526216_yx_exon1_pca0119.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <65.7255> percent units present.
M: <6.46547> percent units marginal.
A: <27.809> percent units absent.
calculating present call for <gsm526217_yx_exon1_pca0120.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.20077e-35
maximum detection p-value = 0.999992
P: <66.1812> percent units present.
M: <6.00065> percent units marginal.
A: <27.8181> percent units absent.
calculating present call for <gsm526218_yx_exon1_pca0122.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.24287e-36
maximum detection p-value = 0.999995
P: <59.7554> percent units present.
M: <6.82603> percent units marginal.
A: <33.4185> percent units absent.
calculating present call for <gsm526219_yx_exon1_pca0123.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 1
P: <64.1731> percent units present.
M: <6.33136> percent units marginal.
A: <29.4956> percent units absent.
calculating present call for <gsm526220_yx_exon1_pca0124.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <61.0365> percent units present.
M: <6.02417> percent units marginal.
A: <32.9393> percent units absent.
calculating present call for <gsm526221_yx_exon1_pca0125.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 0.999977
P: <64.6242> percent units present.
M: <6.10667> percent units marginal.
A: <29.2691> percent units absent.
calculating present call for <gsm526222_yx_exon1_pca0126.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.2164e-36
maximum detection p-value = 1
P: <61.1029> percent units present.
M: <6.11826> percent units marginal.
A: <32.7789> percent units absent.
calculating present call for <gsm526223_yx_exon1_pca0127.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 0.999985
P: <67.0133> percent units present.
M: <5.95922> percent units marginal.
A: <27.0275> percent units absent.
calculating present call for <gsm526224_yx_exon1_pca0128.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.86176e-36
maximum detection p-value = 0.999979
P: <63.5597> percent units present.
M: <6.6677> percent units marginal.
A: <29.7726> percent units absent.
calculating present call for <gsm526225_yx_exon1_pca0129.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.54779e-36
maximum detection p-value = 1
P: <61.2703> percent units present.
M: <6.74669> percent units marginal.
A: <31.983> percent units absent.
calculating present call for <gsm526226_yx_exon1_pca0130.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.10941e-36
maximum detection p-value = 0.999979
P: <49.13> percent units present.
M: <8.12116> percent units marginal.
A: <42.7488> percent units absent.
calculating present call for <gsm526227_yx_exon1_pca0132.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.95044e-35
maximum detection p-value = 1
P: <59.49> percent units present.
M: <5.49123> percent units marginal.
A: <35.0187> percent units absent.
calculating present call for <gsm526228_yx_exon1_pca0133.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <68.1726> percent units present.
M: <5.31709> percent units marginal.
A: <26.5103> percent units absent.
calculating present call for <gsm526229_yx_exon1_pca0134.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 6.61516e-36
maximum detection p-value = 1
P: <57.2691> percent units present.
M: <5.21669> percent units marginal.
A: <37.5142> percent units absent.
calculating present call for <gsm526230_yx_exon1_pca0135.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.32086e-36
maximum detection p-value = 1
P: <62.4064> percent units present.
M: <5.22827> percent units marginal.
A: <32.3653> percent units absent.
calculating present call for <gsm526231_yx_exon1_pca0136.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.70143e-35
maximum detection p-value = 1
P: <51.4124> percent units present.
M: <6.02768> percent units marginal.
A: <42.5599> percent units absent.
calculating present call for <gsm526232_yx_exon1_pca0141.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.66639e-36
maximum detection p-value = 1
P: <64.766> percent units present.
M: <4.86771> percent units marginal.
A: <30.3662> percent units absent.
calculating present call for <gsm526233_yx_exon1_pca0144.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 8.17173e-35
maximum detection p-value = 1
P: <55.5878> percent units present.
M: <5.59269> percent units marginal.
A: <38.8195> percent units absent.
calculating present call for <gsm526234_yx_exon1_pca0145.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999991
P: <70.7354> percent units present.
M: <5.94447> percent units marginal.
A: <23.3201> percent units absent.
calculating present call for <gsm526235_yx_exon1_pca0146.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.66617e-35
maximum detection p-value = 1
P: <58.7566> percent units present.
M: <5.34799> percent units marginal.
A: <35.8954> percent units absent.
calculating present call for <gsm526236_yx_exon1_pca0147.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.53764e-35
maximum detection p-value = 1
P: <67.7112> percent units present.
M: <4.6676> percent units marginal.
A: <27.6212> percent units absent.
calculating present call for <gsm526237_yx_exon1_pca0149.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.97754e-36
maximum detection p-value = 1
P: <63.9751> percent units present.
M: <6.40439> percent units marginal.
A: <29.6206> percent units absent.
calculating present call for
<gsm526238_yx_pca0150_huex_1.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <49.4386> percent units present.
M: <5.99749> percent units marginal.
A: <44.5639> percent units absent.
calculating present call for <gsm526239_yx_exon1_pca0151.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <50.7906> percent units present.
M: <7.34984> percent units marginal.
A: <41.8595> percent units absent.
calculating present call for <gsm526240_yx_exon1_pca0155.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.02653e-35
maximum detection p-value = 1
P: <44.3876> percent units present.
M: <5.93359> percent units marginal.
A: <49.6788> percent units absent.
calculating present call for <gsm526241_yx_exon1_pca0156.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999984
P: <68.7241> percent units present.
M: <6.00486> percent units marginal.
A: <25.271> percent units absent.
calculating present call for <gsm526242_yx_exon1_pca0157.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.53864e-35
maximum detection p-value = 1
P: <61.6471> percent units present.
M: <6.48654> percent units marginal.
A: <31.8664> percent units absent.
calculating present call for <gsm526243_yx_exon1_pca0158.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.56877e-36
maximum detection p-value = 0.999989
P: <61.7436> percent units present.
M: <6.4911> percent units marginal.
A: <31.7653> percent units absent.
calculating present call for <gsm526244_yx_exon1_pca0159.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.65551e-35
maximum detection p-value = 1
P: <60.0777> percent units present.
M: <5.31534> percent units marginal.
A: <34.6069> percent units absent.
calculating present call for <gsm526245_yx_exon1_pca0160.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.97754e-36
maximum detection p-value = 1
P: <57.6068> percent units present.
M: <5.3041> percent units marginal.
A: <37.0891> percent units absent.
calculating present call for <gsm526246_yx_exon1_pca0161.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999987
P: <70.8962> percent units present.
M: <6.0512> percent units marginal.
A: <23.0526> percent units absent.
calculating present call for <gsm526247_yx_exon1_pca0162.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 8.47275e-36
maximum detection p-value = 0.999994
P: <67.2369> percent units present.
M: <5.95044> percent units marginal.
A: <26.8126> percent units absent.
calculating present call for <gsm526248_yx_exon1_pca0163.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999994
P: <61.2461> percent units present.
M: <6.93733> percent units marginal.
A: <31.8166> percent units absent.
calculating present call for <gsm526249_yx_exon1_pca0164.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <53.1232> percent units present.
M: <7.2856> percent units marginal.
A: <39.5912> percent units absent.
calculating present call for <gsm526250_yx_exon1_pca0165.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.2912e-36
maximum detection p-value = 0.999985
P: <63.9031> percent units present.
M: <6.80216> percent units marginal.
A: <29.2948> percent units absent.
calculating present call for <gsm526251_yx_exon1_pca0167.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.06704e-34
maximum detection p-value = 1
P: <53.1611> percent units present.
M: <5.64606> percent units marginal.
A: <41.1928> percent units absent.
calculating present call for <gsm526252_yx_exon1_pca0168.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.18385e-35
maximum detection p-value = 1
P: <60.3547> percent units present.
M: <5.41013> percent units marginal.
A: <34.2351> percent units absent.
calculating present call for <gsm526253_yx_exon1_pca0169.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.66639e-36
maximum detection p-value = 1
P: <58.4628> percent units present.
M: <5.86513> percent units marginal.
A: <35.6721> percent units absent.
calculating present call for <gsm526254_yx_exon1_pca0170.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 1
P: <71.9597> percent units present.
M: <5.82862> percent units marginal.
A: <22.2117> percent units absent.
calculating present call for <gsm526255_yx_exon1_pca0171.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.24287e-36
maximum detection p-value = 0.999992
P: <63.0363> percent units present.
M: <5.10188> percent units marginal.
A: <31.8618> percent units absent.
calculating present call for <gsm526256_yx_exon1_pca0172.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999986
P: <69.58> percent units present.
M: <5.79281> percent units marginal.
A: <24.6272> percent units absent.
calculating present call for <gsm526257_yx_exon1_pca0173.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999996
P: <64.3792> percent units present.
M: <6.09403> percent units marginal.
A: <29.5268> percent units absent.
calculating present call for <gsm526258_yx_exon1_pca0174.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <67.3791> percent units present.
M: <6.53499> percent units marginal.
A: <26.0859> percent units absent.
calculating present call for <gsm526259_yx_exon1_pca0175.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999998
P: <61.1984> percent units present.
M: <6.93065> percent units marginal.
A: <31.871> percent units absent.
calculating present call for <gsm526260_yx_exon1_pca0176.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.97754e-36
maximum detection p-value = 1
P: <60.4169> percent units present.
M: <5.57584> percent units marginal.
A: <34.0073> percent units absent.
calculating present call for <gsm526261_yx_exon1_pca0178.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999994
P: <71.8905> percent units present.
M: <6.09544> percent units marginal.
A: <22.0141> percent units absent.
calculating present call for <gsm526262_yx_exon1_pca0179.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <64.1067> percent units present.
M: <7.36459> percent units marginal.
A: <28.5287> percent units absent.
calculating present call for <gsm526263_yx_exon1_pca0180.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <63.7816> percent units present.
M: <6.93381> percent units marginal.
A: <29.2846> percent units absent.
calculating present call for <gsm526264_yx_exon1_pca0181.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.2164e-36
maximum detection p-value = 0.999997
P: <53.4683> percent units present.
M: <7.18097> percent units marginal.
A: <39.3507> percent units absent.
calculating present call for <gsm526265_yx_exon1_pca0182.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 0.999999
P: <72.058> percent units present.
M: <4.62687> percent units marginal.
A: <23.3152> percent units absent.
calculating present call for <gsm526266_yx_exon1_pca0184.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 1
P: <62.2056> percent units present.
M: <5.77841> percent units marginal.
A: <32.016> percent units absent.
calculating present call for <gsm526267_yx_exon1_pca0187.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 0.999995
P: <61.0927> percent units present.
M: <6.09087> percent units marginal.
A: <32.8164> percent units absent.
calculating present call for <gsm526268_yx_exon1_pca0188.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 1
P: <55.5678> percent units present.
M: <5.32061> percent units marginal.
A: <39.1116> percent units absent.
calculating present call for <gsm526269_yx_exon1_pca0189.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999961
P: <71.8557> percent units present.
M: <5.67309> percent units marginal.
A: <22.4712> percent units absent.
calculating present call for <gsm526270_yx_exon1_pca0190.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <72.3827> percent units present.
M: <5.63131> percent units marginal.
A: <21.986> percent units absent.
calculating present call for <gsm526271_yx_exon1_pca0193.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 1
P: <68.1996> percent units present.
M: <4.88> percent units marginal.
A: <26.9204> percent units absent.
calculating present call for <gsm526272_yx_exon1_pca0194.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999993
P: <74.0703> percent units present.
M: <5.91077> percent units marginal.
A: <20.0189> percent units absent.
calculating present call for <gsm526273_yx_exon1_pca0199.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 1
P: <52.098> percent units present.
M: <6.68174> percent units marginal.
A: <41.2202> percent units absent.
calculating present call for <gsm526274_yx_exon1_pca0200.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999998
P: <62.6568> percent units present.
M: <6.62171> percent units marginal.
A: <30.7215> percent units absent.
calculating present call for <gsm526275_yx_exon1_pca0201.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <59.5715> percent units present.
M: <6.80918> percent units marginal.
A: <33.6193> percent units absent.
calculating present call for <gsm526276_yx_exon1_pca0206.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <63.7528> percent units present.
M: <6.14915> percent units marginal.
A: <30.098> percent units absent.
calculating present call for <gsm526277_yx_exon1_pca0207.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999969
P: <66.0756> percent units present.
M: <6.12423> percent units marginal.
A: <27.8002> percent units absent.
calculating present call for <gsm526278_yx_exon1_pca0208.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.65634e-36
maximum detection p-value = 0.999998
P: <60.7307> percent units present.
M: <7.76271> percent units marginal.
A: <31.5066> percent units absent.
calculating present call for
<gsm526279_yx_pca0209_huex_1.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <48.0087> percent units present.
M: <5.63377> percent units marginal.
A: <46.3576> percent units absent.
calculating present call for
<gsm526280_yx_pca0210_huex_1.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <60.9702> percent units present.
M: <6.10597> percent units marginal.
A: <32.9239> percent units absent.
calculating present call for <gsm526281_yx_exon1_pca0211.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 9.9628e-37
maximum detection p-value = 1
P: <65.0546> percent units present.
M: <5.80194> percent units marginal.
A: <29.1434> percent units absent.
calculating present call for <gsm526282_yx_exon1_pca0213.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 1
P: <68.2337> percent units present.
M: <6.33593> percent units marginal.
A: <25.4304> percent units absent.
calculating present call for
<gsm526283_yx_pca0215_huex_1.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.81121e-36
maximum detection p-value = 1
P: <62.6104> percent units present.
M: <5.27988> percent units marginal.
A: <32.1097> percent units absent.
calculating present call for <gsm526284_yx_exon1_du145.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 0.999994
P: <60.8224> percent units present.
M: <5.50387> percent units marginal.
A: <33.6738> percent units absent.
calculating present call for <gsm526285_yx_exon1_lncap.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999964
P: <61.5909> percent units present.
M: <5.59585> percent units marginal.
A: <32.8133> percent units absent.
calculating present call for
<gsm526286_yx_exon1_lncap104r.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <56.0365> percent units present.
M: <4.58685> percent units marginal.
A: <39.3767> percent units absent.
calculating present call for
<gsm526287_yx_exon1_lncap104s.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.2164e-36
maximum detection p-value = 1
P: <53.8211> percent units present.
M: <4.80382> percent units marginal.
A: <41.375> percent units absent.
calculating present call for <gsm526288_yx_exon1_pc3.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <64.5301> percent units present.
M: <5.14928> percent units marginal.
A: <30.3206> percent units absent.
calculating present call for <gsm526289_yx_exon1_vcap.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999979
P: <69.1201> percent units present.
M: <5.86653> percent units marginal.
A: <25.0133> percent units absent.
calculating present call for <gsm526290_yx_exon1_pan0095.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <67.475> percent units present.
M: <5.06256> percent units marginal.
A: <27.4625> percent units absent.
calculating present call for <gsm526291_yx_exon1_pan0107.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 0.999962
P: <68.3667> percent units present.
M: <5.62429> percent units marginal.
A: <26.009> percent units absent.
calculating present call for <gsm526292_yx_exon1_pan0109.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999995
P: <69.0769> percent units present.
M: <5.40908> percent units marginal.
A: <25.514> percent units absent.
calculating present call for <gsm526293_yx_exon1_pan0110.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999998
P: <70.4002> percent units present.
M: <5.36203> percent units marginal.
A: <24.2378> percent units absent.
calculating present call for <gsm526294_yx_exon1_pan0112.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999999
P: <67.8706> percent units present.
M: <5.40838> percent units marginal.
A: <26.721> percent units absent.
calculating present call for <gsm526295_yx_exon1_pan0113.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <63.5488> percent units present.
M: <5.76788> percent units marginal.
A: <30.6833> percent units absent.
calculating present call for <gsm526296_yx_exon1_pan0114.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.97754e-36
maximum detection p-value = 1
P: <64.179> percent units present.
M: <6.15582> percent units marginal.
A: <29.6651> percent units absent.
calculating present call for <gsm526297_yx_exon1_pan0115.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 1
P: <69.6573> percent units present.
M: <5.49299> percent units marginal.
A: <24.8497> percent units absent.
calculating present call for <gsm526298_yx_exon1_pan0117.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.82454e-35
maximum detection p-value = 1
P: <62.9331> percent units present.
M: <6.23903> percent units marginal.
A: <30.8279> percent units absent.
calculating present call for <gsm526299_yx_exon1_pan0120.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.32086e-36
maximum detection p-value = 0.999994
P: <61.9876> percent units present.
M: <6.17478> percent units marginal.
A: <31.8376> percent units absent.
calculating present call for <gsm526300_yx_exon1_pan0122.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.96887e-35
maximum detection p-value = 1
P: <56.0751> percent units present.
M: <6.21551> percent units marginal.
A: <37.7094> percent units absent.
calculating present call for <gsm526301_yx_exon1_pan0125.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 5.10941e-36
maximum detection p-value = 1
P: <57.6089> percent units present.
M: <6.33733> percent units marginal.
A: <36.0537> percent units absent.
calculating present call for <gsm526302_yx_exon1_pan0127.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.2164e-36
maximum detection p-value = 1
P: <63.2385> percent units present.
M: <5.91604> percent units marginal.
A: <30.8455> percent units absent.
calculating present call for <gsm526303_yx_exon1_pan0128.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999997
P: <67.4736> percent units present.
M: <5.52458> percent units marginal.
A: <27.0019> percent units absent.
calculating present call for <gsm526304_yx_exon1_pan0129.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.95151e-34
maximum detection p-value = 1
P: <56.8088> percent units present.
M: <6.5873> percent units marginal.
A: <36.6039> percent units absent.
calculating present call for <gsm526305_yx_exon1_pan0134.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.32086e-36
maximum detection p-value = 0.999988
P: <67.9798> percent units present.
M: <5.889> percent units marginal.
A: <26.1312> percent units absent.
calculating present call for <gsm526306_yx_exon1_pan0135.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 1.27687e-36
maximum detection p-value = 0.999993
P: <71.1371> percent units present.
M: <4.92529> percent units marginal.
A: <23.9376> percent units absent.
calculating present call for <gsm526307_yx_exon1_pan0136.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.14937e-24
maximum detection p-value = 1
P: <59.4166> percent units present.
M: <6.07332> percent units marginal.
A: <34.51> percent units absent.
calculating present call for <gsm526308_yx_exon1_pan0144.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 4.2164e-36
maximum detection p-value = 1
P: <63.2957> percent units present.
M: <5.4649> percent units marginal.
A: <31.2394> percent units absent.
calculating present call for <gsm526309_yx_exon1_pan0147.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.24287e-36
maximum detection p-value = 1
P: <62.7793> percent units present.
M: <5.61551> percent units marginal.
A: <31.6052> percent units absent.
calculating present call for <gsm526310_yx_exon1_pan0151.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 0.999997
P: <74.1978> percent units present.
M: <4.67918> percent units marginal.
A: <21.123> percent units absent.
calculating present call for <gsm526311_yx_exon1_pan0157.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 0.999985
P: <66.4544> percent units present.
M: <5.03974> percent units marginal.
A: <28.5059> percent units absent.
calculating present call for <gsm526312_yx_exon1_pan0162.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 2.32086e-36
maximum detection p-value = 1
P: <66.2971> percent units present.
M: <5.82476> percent units marginal.
A: <27.8781> percent units absent.
calculating present call for <gsm526313_yx_exon1_pan0164.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <67.5118> percent units present.
M: <5.31218> percent units marginal.
A: <27.176> percent units absent.
calculating present call for <gsm526314_yx_exon1_pan0167.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <68.63> percent units present.
M: <4.93407> percent units marginal.
A: <26.4359> percent units absent.
calculating present call for <gsm526315_yx_exon1_pan0169.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 3.85944e-37
maximum detection p-value = 1
P: <65.3144> percent units present.
M: <5.47087> percent units marginal.
A: <29.2147> percent units absent.
calculating present call for <gsm526316_yx_exon1_pan0171.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <67.2124> percent units present.
M: <4.84911> percent units marginal.
A: <27.9385> percent units absent.
calculating present call for <gsm526317_yx_exon1_pan0172.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <70.7618> percent units present.
M: <5.23108> percent units marginal.
A: <24.0071> percent units absent.
calculating present call for <gsm526318_yx_exon1_pan0174.cel>...
range background of GC-content:
minimum GC-content is 3
maximum GC-content is 25
<284836> of <1432143> calls processed...Finished
detection call statistics:
minimum detection p-value = 7.02165e-37
maximum detection p-value = 1
P: <70.1751> percent units present.
M: <5.37221> percent units marginal.
A: <24.4527> percent units absent.
preprocessing finished.
Opening file </home> in <read> mode...
Opening file </home> in
<read> mode...
Opening file </home> in
<read> mode...
Exporting data from tree <*> to file
</home>...
Reading entries from <huex-1_0-st-v2.anp> ...Finished
<284836> of <284836> records exported.
Opening file </home> in <read> mode...
Opening file </home> in
<read> mode...
Opening file </home> in
<read> mode...
Exporting data from tree <*> to file
</home>...
Reading entries from <huex-1_0-st-v2.anp> ...Finished
<284836> of <284836> records exported.
Killed
====================================
===============================================
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US
[7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xps_1.12.1
-----------------------------------------------------------
Giovanni Lavorgna
DIBIT-HSR
Via Olgettina, 58
20132 Milan Italy
Tel: +39-02-2643-4776
Fax: +39-02-2643-4767
Email: giovanni.lavorgna at hsr.it
________________________________________
Da: cstrato [cstrato at aon.at]
Inviato: luned? 12 settembre 2011 0.00
A: Lavorgna Giovanni
Cc: bioconductor at r-project.org
Oggetto: Re: R: R: R: [BioC] Probe-level analysis of exon arrays using
xps
Dear Giovanni,
As far as I understand you did run rma() and then dabg.call() in the
same R session resulting in a crash in the dabg.call() step. However,
when running dabg.call() first and rma() afterwards there was no
crash.
Is this correct?
To understand the crashes could you please send me the exact code
until
the crash, and also the code which did not crash, thank you.
Best regards
Christian
On 9/11/11 8:38 PM, Lavorgna Giovanni wrote:
> Dear Christian,
>
> many thanks for your answer and for clarifying matters with the
different ROOT releases.
>
> Yes, before I was using root_v5.26.00 without patch and I can
confirm you that the pipeline you designed without the median-polish
sumamrization ran without problems. However, I tried also the more
classical classical rma/dabg approach on my dataset and this time the
script crashed at the end of the rma step without writing the root and
the text file.
>
> I also installed the latest xps_1.12.1 and root_v5.27.04 as you
recommended. As usual, the script without the medpolish step went
fine. Instead, the classical rma/dabg approach ran until the end of
the RMA step, wrote the root and the text files and then crashed.
However, I was still able to get dabg data by running this step before
rma. So I guess I am still able to get what I am looking for.
>
> Thanks again for your help and for making xps available to our
community.
>
> Giovanni
>
>
>
>
> -----------------------------------------------------------
> Giovanni Lavorgna
> DIBIT-HSR
> Via Olgettina, 58
> 20132 Milan Italy
> Tel: +39-02-2643-4776
> Fax: +39-02-2643-4767
> Email: giovanni.lavorgna at hsr.it
> ________________________________________
> Da: cstrato [cstrato at aon.at]
> Inviato: venerd? 2 settembre 2011 21.57
> A: Lavorgna Giovanni
> Cc: bioconductor at r-project.org
> Oggetto: Re: R: R: [BioC] Probe-level analysis of exon arrays using
xps
>
> Dear Giovanni,
>
> I am glad to hear that my suggestions did work for you.
>
> Regarding your questions:
>
> ad 1, Yes, you can change to 'exonlevel="core+extended+affx"'. If
you
> want you can even use 'exonlevel="all"' which is short for
> 'exonlevel="core+extended+full+affx"' (see ?exonLevel).
>
>
> ad 2, Thank you for your report about the memory problems with
> root_v5.28.00. However, please note that the currently recommended
> version in the Description file of xps is root_v5.27.04.
>
> Sadly, the production version root_v5.28.00 had a severe problem
when
> writing a tree, which only appeared when running xps from within R
but
> not when running xps as root macro, see:
> http://root.cern.ch/phpBB3/viewtopic.php?f=3&t=11887&p=51313&sid=5bb
fb7ef1aba101060cc67de9417ea2e#p51313
> For this reason I could not use root_v5.28.00 for the current
release
> and had to ask the BioC maintainers to install root_v5.27.04 on the
BioC
> servers. Thus all users of xps which are downloading the xps binary
must
> install root_v5.27.04 first, and I recommend always that people who
are
> compiling the source themselves, use the officially recommended
version
> of ROOT, too.
>
> Since you do not have a problem with root_v5.26.00 I am wondering if
you
> have installed the patch release of root_v5.26.00, since the
original
> version had a severe memory problem, too, which had only been solved
in
> patch release root_v5.26.00c and later.
>
> BTW, the version of xps, xps_1.8.3, that you mention is pretty old,
> since the current verion for BioC2.8 is xps_1.12.1.
>
> I would recommend that you use xps_1.12.1 with root_v5.27.04, or you
try
> to install the newest production version of ROOT, root_v5.30.01,
which I
> am currently testing with my development version xps_1.13.7. In both
> cases I would be interested to know if you experience any memory
> problems with root.
>
> As you might already know, all versions of root can be downloaded
from:
> ftp://root.cern.ch/root/
>
> I hope this information could clarify these issues.
>
> Best regards
> Christian
>
>
> On 9/2/11 11:08 AM, Lavorgna Giovanni wrote:
>> Dear Christian,
>>
>> I had the chance to use the whole pipeline you designed and it
performed very well. Basically, I got the probe intensities I was
looking using the whole 185 array dataset. However, if you don't
mind, I have a couple of more questions:
>>
>> 1) I would need to check also the probe intensities of a transcript
whose existence is supported only by ESTs. Therefore, it falls in the
"Extended" category. Would it be OK if I change the 'exonlevel'
parameter in this line from:
>>
>> ### 1.step: background - rma
>> > data.bg.rma<- bgcorrect.rma(data.exon, "HuExonRMABgrd",
filedir=datdir,
>> + select="antigenomic", exonlevel="core+affx")
>>
>> to:
>>
>> > data.bg.rma<- bgcorrect.rma(data.exon, "HuExonRMABgrd",
filedir=datdir,
>> + select="antigenomic",
exonlevel="core+extended+affx")
>>
>>
>> and in this other line from:
>>
>> ### 2step: normalization - quantile
>> > data.qu.rma<- normalize.quantiles(data.bg.rma,
"HuExonRMANorm",
>> filedir=datdir ,
>> + exonlevel="core+affx")
>>
>> to:
>>
>> ### 2step: normalization - quantile
>> > data.qu.rma<- normalize.quantiles(data.bg.rma,
"HuExonRMANorm",
>> filedir=datdir ,
>> + exonlevel="core+extended+affx")
>>
>>
>>
>> 2) On my 4Gb Linux system, using xps version 1.8.3, I noticed some
problems.
>> Since ROOT version 5.28, the background correction step steadily
increases memory consumption, until the job is killed by the system
after having completed 142 out of 185 arrays. Memory usage at this
critical point is well over 80%.
>> Instead, up to ROOT version 5.26, using the same test case, memory
occupancy stays consistently under 20% during the run, with the script
smoothly reaching the end. I suspect that a bug related to memory
leakage might have been introduced in version 5.28. Probably, it has
gone unnoticed until now because not many people are analyzing so many
arrays and people that do so might be using systems with much more RAM
than I.
>> My test case is rather big and doesn't easily lend itself to a
bug report to ROOT people. However, you mentioned that you already
observed a lot of disk swapping on your 2Gb system, using the 6 arrays
breast and prostate data from the Affymetrix. I don't know exactly
which root version you are using. However, if you are using the
latest version 5.30 or version 5.28 and by installing ROOT version
5.26 memory usage dramatically drops, this would confirm the bug
existence and would be an excellent test-case to provide to people at
CERN.
>> Please let me know if you would like me to provide more details
about this issue.
>> Thanks again.
>>
>> Giovanni
>>
>> This is the session info (well, before crushing :-) )
>>
>>> sessionInfo()
>> R version 2.11.0 (2010-04-22)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
>> [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US
>> [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods
base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.11.0
>>
>>
>>
>>
>>
>>
>> ____
>> Da: cstrato [cstrato at aon.at]
>> Inviato: domenica 21 agosto 2011 19.56
>> A: Lavorgna Giovanni
>> Cc: bioconductor at r-project.org
>> Oggetto: Re: R: [BioC] Probe-level analysis of exon arrays using
xps
>>
>> Dear Giovanni,
>>
>> I will try to sketch the beginning of your pipeline using a subset
of
>> the Affymetrix exon dataset:
>>
>> First, let me suggest to use the new annotation files version na32
which
>> Affymetrix have just released, to create the scheme file:
>> ### import libary and annotation files
>> > libdir<- "/Volumes/GigaDrive/Affy/libraryfiles"
>> > anndir<- "/Volumes/GigaDrive/Affy/Annotation"
>> > scmdir<- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes/na32"
>> > scheme.exon<- import.exon.scheme("huex10stv2", filedir =
scmdir,
>> + file.path(libdir, "HuEx-1_0-st-v2_libraryfile",
>> "HuEx-1_0-st-r2", "HuEx-1_0-st-v2.r2.clf"),
>> + file.path(libdir, "HuEx-1_0-st-v2_libraryfile",
>> "HuEx-1_0-st-r2", "HuEx-1_0-st-v2.r2.pgf"),
>> + file.path(anndir, "Version11Jul",
>> "HuEx-1_0-st-v2.na32.hg19.probeset.csv"),
>> + file.path(anndir, "Version11Jul",
>> "HuEx-1_0-st-v2.na32.hg19.transcript.csv"))
>>
>> For this example I import the breast and prostate data from the
>> Affymetrix exon dataset:
>> ### import CEL-files
>> > celdir<- "/Volumes/GigaDrive/ChipData/Exon/HuMixture"
>> > datdir<- getwd()
>> > celfiles<-
>> c("huex_wta_breast_A.CEL","huex_wta_breast_B.CEL","huex_wta_breast_
C.CEL",
>> +
>> "huex_wta_prostate_A.CEL","huex_wta_prostate_B.CEL","huex_wta_prost
ate_C.CEL")
>> > celnames<-
>>
c("BreastA","BreastB","BreastC","ProstateA","ProstateB","ProstateC")
>> > data.exon<- import.data(scheme.exon, "HuMixtureExon",
filedir=datdir,
>> + celdir=celdir, celfiles=celfiles, celnames=celnames)
>>
>> Now I suggest to start a new R-session for preprocessing:
>> ### first, load ROOT scheme file and ROOT data file
>> > scmdir<- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes/na32"
>> > scheme.exon<-
root.scheme(file.path(scmdir,"huex10stv2.root"))
>> > datdir<- getwd()
>> > data.exon<- root.data(scheme.exon,
>> file.path(datdir,"HuMixtureExon_cel.root"))
>> > str(data.exon)
>>
>> ### 1.step: background - rma
>> > data.bg.rma<- bgcorrect.rma(data.exon, "HuExonRMABgrd",
filedir=datdir,
>> + select="antigenomic", exonlevel="core+affx")
>>
>> ### 2step: normalization - quantile
>> > data.qu.rma<- normalize.quantiles(data.bg.rma,
"HuExonRMANorm",
>> filedir=datdir ,
>> + exonlevel="core+affx")
>>
>> ### 3.step: summarization - medpol (not necessary in your case)
>> #data.mp.rma<- summarize.rma(data.qu.rma, "HuExonRMASum",
filedir=datdir,
>> # exonlevel="core+affx")
>>
>> To dump the probes to a text file you simply do:
>> ### export normalized probes intensities
>> > export(data.qu.rma, treetype="cqu", varlist = "fInten",
>> + outfile=paste(datdir, "BreastProstate_cqu.txt", sep="/"))
>>
>> Now you have table "BreastProstate_cqu.txt" containing the
>> (X,Y)-coordinates followed by the normalized intensities for each
>> sample. However, please note that for 6 samples this file has
already a
>> size of 180 MB, thus for your 185 samples it will probably have a
size
>> of more than 4 GB. Thus it is not quite clear to me how you want to
proceed.
>>
>> Nevertheless, since you are interested in selected transcripts
only, you
>> need to get the (X,Y)-coordinates for these transcripts in order to
>> extract the intensities from the table. Let us assume that you want
to
>> get the (X,Y)-coordinates for the CD44 gene. For this purpose you
have
>> three options:
>>
>> 1, If you are using the development version xps_1.13.6, which will
be
>> available for download from the BioC development site in a few
days, you
>> can do the following:
>> ### get internal UNIT_ID for CD44
>> > id<- symbol2unitID(scheme.exon, symbol="CD44",
>> unittype="transcript", as.list =TRUE)
>> > id
>> $`3326635`
>> [1] "185195"
>>
>> $`3326730`
>> [1] "185196"
>>
>> ### attach (x,y)-coordinates for all UNIT_IDs
>> > data.qu.rma<- attachDataXY(data.qu.rma)
>>
>> ### get (x,y)-coordinates for CD44
>> > xy<- indexUnits(data.qu.rma, which="core+affx",
unitID=unlist(id))
>> Error in .local(object, ...) : only 1 of 2 UNIT_ID are valid
>>
>> The reason for this error is that only transcript_cluster_id
"3326635"
>> belongs to level "core" while "3326730" belongs to level
"extended".
>> Thus you need to do:
>> > xy<- indexUnits(data.qu.rma, which="core+affx",
unitID=id[[1]])
>> > dim(xy)
>> [1] 103 4
>> > head(xy)
>> UNIT_ID X Y XY
>> 3151152 185195 1638 388 994919
>> 3151153 185195 2407 79 204648
>> 3151154 185195 2393 882 2260314
>> 3151155 185195 1728 1223 3132609
>> 3151156 185195 1843 1404 3596084
>> 3151157 185195 1369 2167 5548890
>>
>> Now you have the (X,Y)-coordinates for the CD44 gene which you can
use
>> to get the normalized intensities from table
"BreastProstate_cqu.txt".
>>
>>
>> 2, If you would have enough RAM and the new version xps_1.13.6 then
the
>> most simple way would be to attach the data. In the following I
will
>> attach only the first two trees, however this causes already a lot
of
>> swapping on my Mac with 2GB RAM:
>> ### attach data for 2 trees
>> > treenames<- unlist(treeNames(data.qu.rma))
>> > data.qu.rma<- attachInten(data.qu.rma,
treenames=treenames[1:2])
>>
>> ## get the normalized intensities for CD44
>> > data<- validData(data.qu.rma, which="core+affx",
unitID=185195)
>> > dim(data)
>> [1] 103 2
>> > head(data)
>> BreastA.cqu_MEAN BreastB.cqu_MEAN
>> 994919 29.51080 3.60245
>> 204648 4.94509 58.01030
>> 2260314 25.84620 2.86042
>> 3132609 2.91305 3.93297
>> 3596084 123.34400 147.01000
>> 5548890 434.51000 367.34400
>>
>> ### remove the data
>> > data.qu.rma<- removeInten(data.qu.rma)
>>
>>
>> 3, With the current version of xps extracting the (X,Y)-coordinates
for
>> the CD44 gene is more complicated:
>> First you need to get the transcript_cluster_id for CD44:
>> > ann<- export(scheme.exon, treetype="ann",
>> varlist="fTranscriptID:fSymbol",
>> + as.dataframe=TRUE, outfile="tmp_ann.txt")
>> > id<- split(ann[,"GeneSymbol"], ann[,"TranscriptClusterID"]);
>> > id<- lapply("CD44", function(x) names(which(id == x)));
>> > id
>> [[1]]
>> [1] "3326635" "3326730"
>>
>> Then you need to get the internal UNIT_ID:
>> > idx<- export(scheme.exon, treetype="idx",
>> varlist="fUnitName:fTranscriptID",
>> + as.dataframe=TRUE, outfile="tmp_idx.txt")
>> > unitid<- split(idx[,"UnitName"], idx[,"UNIT_ID"]);
>> > unitid<- lapply(unlist(id), function(x) names(which(unitid
== x)));
>> > unitid
>> [[1]]
>> [1] "185195"
>>
>> [[2]]
>> [1] "185196"
>>
>> Finally you need to get the (X,Y)-coordinates for "3326635" only:
>> > scm<- export(scheme.exon, treetype="scm",
varlist="fUnitID:fX:fY:fMask",
>> + as.dataframe=TRUE, outfile="tmp_scm.txt")
>> > xy<- scm[which(scm[,"UNIT_ID"] == unlist(unitid)[1]),]
>> > dim(xy)
>> [1] 365 4
>>
>> As you see dim(xy) has more rows than above, thus you need to get
the
>> "core" subset only (see ?exonLevel):
>> > unique(xy[,"Mask"])
>> [1] 8192 1024 2048 256 512 4096
>> > xy<- rbind(xy[which(xy[,"Mask"] == 8192),],
xy[which(xy[,"Mask"] ==
>> 1024),])
>> > dim(xy)
>> [1] 103 4
>> > head(xy)
>> UNIT_ID X Y Mask
>> 3151152 185195 1638 388 8192
>> 3151153 185195 2407 79 8192
>> 3151154 185195 2393 882 8192
>> 3151155 185195 1728 1223 8192
>> 3151216 185195 1781 15 8192
>> 3151217 185195 1442 762 8192
>>
>> Now you have the (X,Y)-coordinates for the CD44 gene as above.
>>
>>
>> ad a) Remove probes that hybridize to multiple loci in the genome:
>>
>> I do not know how you want to remove these probes, however you can
get
>> the sequences of all probes from the following table:
>> > export(scheme.exon, treetype="prb")
>>
>> Furthermore, when exporting the probeset annotation by:
>> > export(scheme.exon, treetype="anp")
>> you will see that the table contains column "CrossHybType" (see the
Affy
>> README file for exon arrays). Only crosshyb_type = 1 (unique) does
>> contain unique probesets.
>>
>> Please let me know if this is the info you were looking for.
>>
>> Best regards
>> Christian
>>
>>
>> On 8/18/11 11:48 PM, Lavorgna Giovanni wrote:
>>> Dear Cristian,
>>> many thanks for your prompt answer. In my case, once I have the
probe intensities, I would like to do the following two preliminary
steps:
>>> a) Remove probes that hybridize to multiple loci in the genome.
>>> b) Remove probes that show a correlation coefficient below a
certain threshold.
>>> Then, I would like to calculate the differential expression in
diseased vs. healthy samples for a few transcripts of mine by
averaging the ratio of the probe intensities. I hope that the
increased granularity and the reduced background of this method can
give a better resolution to my analysis. As I said before, similar
probe selection methods have been already described (see for example
Xing Y, Kapur K, Wong WH. PLoS ONE. 2006 20;1:e88) and applied to
genome wide studies.
>>>
>>> In my case, after step a), I would like simply to dump the probes
to a text file, select those of my interest and read them into to a
spreadsheet in order to calculate the correlation coefficient and the
fold-change of my transcripts. You already started to sketch the
beginning of pipeline I should use: if I am not asking for too much, I
would be grateful if you could elaborate it a little more to include
also these final two steps.
>>> Thanks again for your assistance and keep up the good work.
>>> Giovanni
>>>
>>> ________________________________________
>>> Da: cstrato [cstrato at aon.at]
>>> Inviato: gioved? 18 agosto 2011 20.28
>>> A: Lavorgna Giovanni
>>> Cc: bioconductor at r-project.org
>>> Oggetto: Re: [BioC] Probe-level analysis of exon arrays using xps
>>>
>>> Dear Giovanni,
>>>
>>> In principle you could do the background and normalization steps
>>> separately, e.g.:
>>> > data.bg.rma<- bgcorrect.rma(data.exon, ...)
>>> > data.qu.rma<- normalize.quantiles(data.bg.rma, ...)
>>>
>>> Now you have the normalized probes, however, you cannot do any
>>> summarization such as median-polish or mean.
>>>
>>> It is not quite clear to me how you want to proceed with the
normalized
>>> probe intensities?
>>>
>>> Best regards
>>> Christian
>>> _._._._._._._._._._._._._._._._._._
>>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
>>> V.i.e.n.n.a A.u.s.t.r.i.a
>>> e.m.a.i.l: cstrato at aon.at
>>> _._._._._._._._._._._._._._._._._._
>>>
>>>
>>> On 8/18/11 7:08 PM, Lavorgna Giovanni wrote:
>>>>
>>>> As you guys know, there is a growing evidence showing that a
probe-level analysis (as opposed to a probeset-level or a gene-level
analysis) could be useful in analyzing Exon arrays. I am currently
analyzing several human exon chips (185!) on a 4 GB machine and I am
using the xps package. I would like to stick to this software since it
allows to manage several chips with the resources at hand and I was
wondering if anyone has ever tried to perform probe level analysis
using xps. Also, I would be grateful if anyone could point out
alternative resources to perform this job.
>>>> Thanks in advance.
>>>> Giovanni
>>>>
>>>>
>>>>
>>>>
>>>> -----------------------------------------------------------------
>>>>
>>>> Dai il tuo 5XMILLE al San Raffaele. Basta una firma.
>>>> Se firmi per la ricerca sanitaria del San Raffaele di Milano,
firmi per tutti.
>>>> C.F. 03 06 42 80 153.
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>>>>
>>>> _______________________________________________
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http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>> -----------------------------------------------------------------
>>>
>>> Dai il tuo 5XMILLE al San Raffaele. Basta una firma.
>>> Se firmi per la ricerca sanitaria del San Raffaele di Milano,
firmi per tutti.
>>> C.F. 03 06 42 80 153.
>>> INFO: 5xmille at hsr.it - www.5xmille.org
>>>
>>
>