Entering edit mode
Hi Andreas,
Thanks for replying. If I can fix the problem with virtualArrays I
will
cite for sure. Here is the information for expression matrices from
both
datasets:
>head(exprs(AF.mydata))
10.5A.CEL 10.5B.CEL 10.5C.CEL 11.5A.CEL 11.5B.CEL 11.5C.CEL
12.5A.CEL 12.5B.CEL 12.5C.CEL E17.5A.CEL
1 105 128 104 114 159 227
129 158 182 74
2 14320 19105 11777 14959 19861 17099
14849 21567 20675 9377
3 127 187 115 187 163 455
165 269 244 79
4 14927 19889 11911 15203 19997 18227
15369 22589 20806 9655
5 92 150 88 73 103 259
89 113 234 83
6 110 98 113 139 144 161
98 132 159 61
E17.5B.CEL E17.5C.CEL E17.5D.CEL E17.5E.CEL E19.5A_.CEL E19.5B.CEL
E19.5C.CEL P0A.CEL P0B.CEL P0C.CEL
1 78 68 72 60 134 223
120 75 69 65
2 9395 9786 10567 10824 10034 8349
10384 7492 6381 8700
3 120 117 140 127 205 231
248 96 66 83
4 9597 9972 10903 11056 10381 8328
10232 7591 6465 8420
5 61 76 63 50 136 176
102 73 60 84
6 74 58 65 74 130 172
127 91 49 63
P0D.CEL P0E.CEL P28A.CEL P28B.CEL P28C.CEL P2A.CEL P2B.CEL P2C.CEL
WB_AF_A.CEL WB_AF_B.CEL WB_AF_C.CEL
1 68 59 71 77 56 166 168 185
172 158 96
2 7272 9501 46 49 41 14202 13199 13267
18186 14627 13158
3 85 160 78 65 58 210 214 196
189 158 151
4 7524 9664 57 55 46 14759 13533 14263
18918 15468 13308
5 64 72 41 46 44 144 192 138
145 194 106
6 65 68 88 76 58 156 149 177
119 145 109
>head(exprs(IL.mydataA))
P4_C1 P4_C2 P4_C3 T1
T2 T3 P30_C1
T.kvUVfFyruaCeqZVs -4.704992 -5.008878 4.013575 -7.155298
-1.018183 -0.5739443 -1.218571
Q96MoiqM_z49FU37tE -5.498747 4.351016 7.339304 6.459189
1.064443 1.2691800 -7.323681
WpaZ9x9f_hAnoR.VBE 2483.110000 2872.099000 2461.915000 2399.139000
3167.442000 2507.4980000 3831.747000
ZhdXp75JftSF3iWLF4 467.483700 564.803300 502.616200 429.565400
848.511400 473.4642000 690.122100
QoJVn30kwRGJ3SN9Q4 5.977465 8.649684 -6.068388 -2.379038
-3.892618 -0.8772737 -1.730694
xnx7ijE2CcOSlY55eA 525.841000 588.122100 577.280500 493.595600
540.728800 559.2224000 713.712900
P30_C2 P30_C3 51 55
56
T.kvUVfFyruaCeqZVs 1.4039610 -7.777119 -8.5276410 -9.3387030
-0.5762033
Q96MoiqM_z49FU37tE -0.2668989 4.637646 -0.4015962 -0.8310394
1.8641310
WpaZ9x9f_hAnoR.VBE 3169.7620000 3210.845000 3391.7170000 3615.6720000
2988.9270000
ZhdXp75JftSF3iWLF4 577.8732000 580.200300 582.7916000 654.7377000
616.9252000
QoJVn30kwRGJ3SN9Q4 -3.8180120 7.699070 -5.1443480 2.5087130
-2.0737350
xnx7ijE2CcOSlY55eA 335.6019000 463.035400 657.2077000 717.1554000
522.6875000
Waiting for your reply
Best
AK
On 06-Jun-13 3:38 AM, Andreas Heider wrote:
> Dear Atul,
> first of all: Thanks for using my package!
> I think the error you get directly relates to your Illumina Dataset.
> Can you send me a "head()" of the expression matrices of both
> datasets? Then we will see the problem there. There are several way
to
> load in Illumina datasets, and we need to use the right one.
>
> Please, do not hessitate to contact me again. And please cite my
work in:
> http://www.biomedcentral.com/1471-2105/14/75
>
> Yours sincerely,
> Andreas Heider
>
>
> 2013/5/31 Atul Kakrana <atulkakrana@outlook.com> <mailto:atulkakrana@outlook.com>>
>
> Hi Andreas (and everybody),
>
> I am using virtualArray package to combine Illumina and
Affymetrix
> micro-array datasets. As mentioned in the virtualArray manual
and
> publication I prepared 'ExpressionSet' from both affymetrix and
> Illumina datasets. But while compiling a 'virtualarray' I get an
> error.
>
> MINIMAL CODE:
>
> IL.mydata <- lumiR.batch(filelist)
> AF.mydata <- ReadAffy()
>
> AF.eset.BG <http: af.eset.bg=""> <- bg.correct.rma(AF.mydata)
> IL.eset.BG <http: il.eset.bg=""> <- lumiB(IL.mydata, method =
> c('bgAdjust.affy'))
>
> virtArrays.EB <-
> virtualArrayExpressionSets(all_expression_sets=c('AF.eset.BG
> <http: af.eset.bg="">','IL.eset.BG
<http: il.eset.bg="">'),identifier
> = 'SYMBOL')
>
>
> SCREEN OUTPUT/ERROR:
>
> >virtArrays.EB <-
virtualArrayExpressionSets(all_expression_sets=c('AF.eset.BG
<http: af.eset.bg="">','IL.eset.BG <http: il.eset.bg="">'),identifier =
'SYMBOL')
>
> Now preprocessing raw data ofAF.eset.BG <http: af.eset.bg=""> :
Loading annotations...
>
> Now preprocessing raw data ofAF.eset.BG <http: af.eset.bg=""> :
Collapsing expression values to their median ...
> Using identifier as id variables
>
> Now preprocessing raw data ofAF.eset.BG <http: af.eset.bg=""> :
Annotating expression values with SYMBOL ...
>
> Size of expression matrix ofAF.eset.BG <http: af.eset.bg=""> :
22051 rows and 31 columns
>
> Now preprocessing raw data ofIL.eset.BG <http: il.eset.bg=""> :
Loading annotations...
>
> Now preprocessing raw data ofIL.eset.BG <http: il.eset.bg=""> :
Collapsing expression values to their median ...
> Using identifier as id variables
>
> Now preprocessing raw data ofIL.eset.BG <http: il.eset.bg=""> :
Annotating expression values with SYMBOL ...
>
> Size of expression matrix ofIL.eset.BG <http: il.eset.bg=""> :
19443 rows and 6 columns
>
> Matching and merging all data sets. This could take some time...
>
> Size of expression matrix of whole dataset: 16536 rows and 37
columns
>
> Now combining pData of all data sets...
>
> Now setting up pData ofAF.eset.BG <http: af.eset.bg=""> ...
>
> Now setting up pData ofIL.eset.BG <http: il.eset.bg=""> ...
>
> The file 'sample_info.txt' has been written to your current
working directory. Please modify it appropriately!
>
> Using only 'Batch' column as information for batch effect
removal.
> Reading Sample Information File
> Reading Expression Data File
> Found 2 batches
> Found 0 covariate(s)
> Found 544800 Missing Data Values
> Standardizing Data across genes
> Error in solve.default(t(des) %*% des) :
> Lapack routine dgesv: system is exactly singular: U[1,1] = 0
>
>
> I am not being able to understand the reason behind the error
and
> would really appreciate help on this. I have come across few
> potential bugs in virtualArrays pack too which I will post once
> done with this part.
>
> Session Info:
>
> >sessionInfo()
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
base
>
> other attached packages:
> [1] lumiMouseAll.db_1.18.0 lumi_2.10.0 nleqslv_2.0
mouse4302.db_2.8.1
> [5] org.Mm.eg.db_2.8.0 RSQLite_0.11.4 DBI_0.2-7
AnnotationDbi_1.20.7
> [9] Biobase_2.18.0 BiocGenerics_0.4.0
virtualArray_1.2.1 preprocessCore_1.20.0
> [13] plyr_1.8
>
> loaded via a namespace (and not attached):
> [1] affy_1.36.1 affyio_1.26.0 affyPLM_1.34.0
annotate_1.36.0
> [5] BiocInstaller_1.8.3 Biostrings_2.26.3 colorspace_1.2-2
gcrma_2.30.0
> [9] GEOquery_2.24.1 grid_2.15.3 IRanges_1.16.6
KernSmooth_2.23-10
> [13] lattice_0.20-15 MASS_7.3-23 Matrix_1.0-12
methylumi_2.4.0
> [17] mgcv_1.7-23 nlme_3.1-108 parallel_2.15.3
RCurl_1.95-4.1
> [21] reshape2_1.2.2 splines_2.15.3 stats4_2.15.3
stringr_0.6.2
> [25] tools_2.15.3 XML_3.96-1.1 xtable_1.7-1
zlibbioc_1.4.0
>
>
> Thanks
>
> A.
>
>
>
>
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