Hi! I have Illumina data for analysis that is produced with BeadStudio v3. It is not background corrected and also not normalized. I wanted to try the lumi package and I found a previous posting to the mailing list describing how to read in the control data from a separate file h ttp://article.gmane.org/gmane.science.biology.informatics.conductor/15 391/match=gordon+background+correction+lumi I did the same (as far as I can tell) > rawX=lumiR("raw_data.txt") > controlgp=lumiR("qcinfo.txt") > rawX at controlData=as.data.frame(exprs(controlgp)) > rawXbgc=lumiB(rawX,method="bgAdjust") Here is what I have in rawX > exprs(rawX[1:5,1:8]) 1881436004_A 1881436004_B 1881436004_C 1881436009_A 1881436009_B 1881436009_C 1881436049_A 1881436049_B 20605 270.30210 252.15860 271.25070 277.39090 249.06970 221.26020 223.3545 231.69390 3450747 483.33750 423.05290 460.44330 547.50350 462.51610 439.66790 408.1301 433.04090 3060450 620.23050 621.86890 626.29790 703.47220 562.79860 483.12060 523.9857 571.69780 870131 78.45721 71.16602 67.74918 75.95979 75.14289 74.56358 80.1152 74.99714 5310368 90.98277 79.14721 82.17856 85.82687 89.79446 81.63494 80.4482 74.59328 Here is part of my @controlData > rawX at controlData 1881436004_A 1881436004_B 1881436004_C 1881436004_D 1881436004_E 1881436004_F 1881436009_A BIOTIN 6683.65000 6280.45700 5796.20100 6058.32500 5540.00200 6039.07700 6612.78700 CY3_HYB 13238.52000 12945.04000 12741.06000 12797.29000 11272.87000 12798.53000 12288.96000 HIGH_STRINGENCY_HYB 31363.13000 33693.30000 31494.96000 32456.38000 29554.45000 31253.40000 29861.95000 HOUSEKEEPING 20446.56000 19445.20000 19390.52000 19781.67000 18907.65000 19454.81000 20602.37000 LABELING 85.73669 78.42913 82.58459 79.09451 80.69878 80.78196 90.47139 LOW_STRINGENCY_HYB 13349.75000 12996.49000 12820.47000 12872.48000 11340.68000 12900.72000 12363.55000 NEGATIVE 84.07156 80.37030 83.57912 79.34184 80.80109 78.84014 So why does lumiB then subtract CY3_HYB from the original values because that seems to have happened here????? > exprs(rawXbgc[1:5,1:8]) 1881436004_A 1881436004_B 1881436004_C 1881436009_A 1881436009_B 1881436009_C 1881436049_A 1881436049_B 20605 -12968.22 -12692.88 -12469.81 -12011.57 -13004.72 -12574.24 -11326.32 -10950.92 3450747 -12755.18 -12521.99 -12280.62 -11741.46 -12791.27 -12355.83 -11141.54 -10749.57 3060450 -12618.29 -12323.17 -12114.76 -11585.49 -12690.99 -12312.38 -11025.68 -10610.91 870131 -13160.06 -12873.87 -12673.31 -12213.00 -13178.65 -12720.94 -11469.55 -11107.61 5310368 -13147.54 -12865.89 -12658.88 -12203.13 -13164.00 -12713.87 -11469.22 -11108.02 If you have trouble reading the columns, here an example with the first datapoint: 270.30210-13238.52000 = -12968.22 What should have happened is subtraction of average value of negative control values so sth like 80. Here is the session info if that is useful: R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_1.4.0 annotate_1.16.1 xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-4 [6] DBI_0.2-4 mgcv_1.3-29 affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 [11] Biobase_1.16.2 Could this be sth wrong with my file? Anyone able to point me to the problem? Thanks! Merja ########################################### This message has been scanned by F-Secure Anti-Virus for...{{dropped:4}}

Hi Merja, We have added some control probe related functions in the developing version of lumi. Now, you can easily input and plot the control probe information output by BeadStudio. Related functions include: "getControlData" "addControlData2lumi" "plotControlData" "plotHousekeepingGene" "plotStringencyGene" We will add more detailed description in the vignette later. As it is still under improvement, any suggestions are welcome. You can get the source code from: http://www.bioconductor.org/packages/2.2/bioc/html/lumi.html Pan On 1/15/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Message: 1 > Date: Mon, 14 Jan 2008 12:07:49 +0100 > From: "merja matilainen" <merja.matilainen at="" uni.lu=""> > Subject: [BioC] Lumi package: control data for background correction > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <46B6E4B75821C449868D25354BE0839F84628B at solo.uni.lux> > Keywords: disclaimer > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > > I have Illumina data for analysis that is produced with BeadStudio v3. It is > not background corrected and also not normalized. I wanted to try the lumi > package and I found a previous posting to the mailing list describing how to > read in the control data from a separate file > http://article.gmane.org/gmane.science.biology.informatics.conductor /15391/mat > ch=gordon+background+correction+lumi > > I did the same (as far as I can tell) >> rawX=lumiR("raw_data.txt") >> controlgp=lumiR("qcinfo.txt") >> rawX at controlData=as.data.frame(exprs(controlgp)) >> rawXbgc=lumiB(rawX,method="bgAdjust") > > Here is what I have in rawX >> exprs(rawX[1:5,1:8]) > 1881436004_A 1881436004_B 1881436004_C 1881436009_A 1881436009_B > 1881436009_C 1881436049_A 1881436049_B > 20605 270.30210 252.15860 271.25070 277.39090 249.06970 > 221.26020 223.3545 231.69390 > 3450747 483.33750 423.05290 460.44330 547.50350 462.51610 > 439.66790 408.1301 433.04090 > 3060450 620.23050 621.86890 626.29790 703.47220 562.79860 > 483.12060 523.9857 571.69780 > 870131 78.45721 71.16602 67.74918 75.95979 75.14289 > 74.56358 80.1152 74.99714 > 5310368 90.98277 79.14721 82.17856 85.82687 89.79446 > 81.63494 80.4482 74.59328 > > > Here is part of my @controlData >> rawX at controlData > 1881436004_A 1881436004_B 1881436004_C 1881436004_D > 1881436004_E 1881436004_F 1881436009_A > BIOTIN 6683.65000 6280.45700 5796.20100 6058.32500 > 5540.00200 6039.07700 6612.78700 > CY3_HYB 13238.52000 12945.04000 12741.06000 12797.29000 > 11272.87000 12798.53000 12288.96000 > HIGH_STRINGENCY_HYB 31363.13000 33693.30000 31494.96000 32456.38000 > 29554.45000 31253.40000 29861.95000 > HOUSEKEEPING 20446.56000 19445.20000 19390.52000 19781.67000 > 18907.65000 19454.81000 20602.37000 > LABELING 85.73669 78.42913 82.58459 79.09451 > 80.69878 80.78196 90.47139 > LOW_STRINGENCY_HYB 13349.75000 12996.49000 12820.47000 12872.48000 > 11340.68000 12900.72000 12363.55000 > NEGATIVE 84.07156 80.37030 83.57912 79.34184 > 80.80109 78.84014 > > So why does lumiB then subtract CY3_HYB from the original values because that > seems to have happened here????? >> exprs(rawXbgc[1:5,1:8]) > 1881436004_A 1881436004_B 1881436004_C 1881436009_A 1881436009_B > 1881436009_C 1881436049_A 1881436049_B > 20605 -12968.22 -12692.88 -12469.81 -12011.57 -13004.72 > -12574.24 -11326.32 -10950.92 > 3450747 -12755.18 -12521.99 -12280.62 -11741.46 -12791.27 > -12355.83 -11141.54 -10749.57 > 3060450 -12618.29 -12323.17 -12114.76 -11585.49 -12690.99 > -12312.38 -11025.68 -10610.91 > 870131 -13160.06 -12873.87 -12673.31 -12213.00 -13178.65 > -12720.94 -11469.55 -11107.61 > 5310368 -13147.54 -12865.89 -12658.88 -12203.13 -13164.00 > -12713.87 -11469.22 -11108.02 > > If you have trouble reading the columns, here an example with the first > datapoint: 270.30210-13238.52000 = -12968.22 > > What should have happened is subtraction of average value of negative control > values so sth like 80. > > Here is the session info if that is useful: > > R version 2.6.1 (2007-11-26) > i386-apple-darwin8.10.1 > > locale: > C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_1.4.0 annotate_1.16.1 xtable_1.5-2 > AnnotationDbi_1.0.6 RSQLite_0.6-4 > [6] DBI_0.2-4 mgcv_1.3-29 affy_1.16.0 > preprocessCore_1.0.0 affyio_1.6.1 > [11] Biobase_1.16.2 > > > Could this be sth wrong with my file? Anyone able to point me to the problem? > > Thanks! > > Merja > ########################################### > > This message has been scanned by F-Secure Anti-Virus for...{{dropped:4}} > --------------------------------------------------- Pan Du, PhD Research Assistant Professor Robert H. Lurie Comprehensive Cancer Center Northwestern University 676 ST Clair St., #1200 Chicago, IL 60611 Office (312)695-4781 dupan at northwestern.edu