Hi, I am trying to annotate my illumina microarray using the following script that I found online. However, I am having some difficulties with it as it is not writing out the annotation data with the normalised data. Also, using this script means that I don't know how to load in the sample file info. I have copied the script that I used and the R output and session info below. Any help would be greatly appreciated. Script: > library(lumi) > fileName <- 'raw_data_lumi_21.txt' > katie.lumi = lumiR(fileName, convertNuID=FALSE) > katie.lumi = addNuID2lumi(katie.lumi, + annotationFile='HUMANREF-8_V3_0_R1_11282963_A_WGDASL', + annotationColName=c(sequence='Probe_Sequence', probe='Probe_Id', symbol='Symbol')) > katie.lumi > summary(katie.lumi, 'QC') > lumi.T <- lumiT(katie.lumi) > lumi.N <- lumiN(lumi.T) > lumi.N.Q <- lumiQ(lumi.N) > summary(lumi.N.Q, 'QC') > write.exprs(lumi.N.Q, file='normkatieData21anno.txt') R output: > library(lumi) Loading required package: annotate Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affy Loading required package: mgcv This is mgcv 1.6-1. For overview type `help("mgcv-package")'. Loading required package: preprocessCore Loading required package: RSQLite Loading required package: DBI Loading required package: MASS > fileName <- 'raw_data_lumi_21.txt' > katie.lumi = lumiR(filename, sampleInfoFile='sample_table_21.txt', convertNuID=FALSE) Error in file.exists(fileName) : object 'filename' not found > katie.lumi = lumiR(fileName, sampleInfoFile='sample_table_21.txt', convertNuID=FALSE) Error in read.table(file = fileName, header = TRUE, sep = sep, dec = dec, : unused argument(s) (sampleInfoFile = "sample_table_21.txt") > katie.lumi = lumiR(fileName, convertNuID=FALSE) Perform Quality Control assessment of the LumiBatch object ... > katie.lumi = addNuID2lumi(katie.lumi, + annotationFile='HUMANREF-8_V3_0_R1_11282963_A_WGDASL', + annotationColName=c(sequence='Probe_Sequence', probe='Probe_Id', symbol='Symbol')) Directly converting probe sequence to nuIDs ... > katie.lumi Summary of data information: Data File Information: Major Operation History: submitted finished 1 2010-05-21 12:28:46 2010-05-21 12:29:12 2 2010-05-21 12:29:12 2010-05-21 12:29:13 3 2010-05-21 12:30:14 2010-05-21 12:30:19 4 2010-05-21 12:30:14 2010-05-21 12:30:19 5 2010-05-21 12:30:14 2010-05-21 12:30:19 command 1 lumiR("raw_data_lumi_21.txt", convertNuID = FALSE) 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) 3 addNuID2lumi(x.lumi = katie.lumi, annotationFile = "HUMANREF- 8_V3_0_R1_11282963_A_WGDASL", 4 annotationColName = c(sequence = "Probe_Sequence", probe = "Probe_Id", 5 symbol = "Symbol")) lumiVersion 1 1.14.0 2 1.14.0 3 1.14.0 4 1.14.0 5 1.14.0 Object Information: LumiBatch (storageMode: lockedEnvironment) assayData: 24526 features, 21 samples element names: detection, exprs, se.exprs protocolData: none phenoData sampleNames: NC37, NC54, ..., KT27P (21 total) varLabels and varMetadata description: sampleID: The unique Illumina microarray Id featureData featureNames: Ku8QhfS0n_hIOABXuE, fqPEquJRRlSVSfL.8A, ..., N8t5EuJCr0Tk9.zHno (24526 total) fvarLabels and fvarMetadata description: ProbeID: The Illumina microarray identifier TargetID: The Illumina TargetID ...: ... PROBE_COORDINATES: PROBE_COORDINATES (8 total) experimentData: use 'experimentData(object)' Annotation: lumiHumanAll.db Control Data: Available QC information: Please run summary(x, 'QC') for details! > summary(katie.lumi, 'QC') Data dimension: 24526 genes x 21 samples Summary of Samples: NC37 NC54 NC2 NC5 HP13 HP3 mean 8.8950 7.8930 8.8250 9.0190 9.3190 9.6140 standard deviation 2.5030 2.7780 2.5320 2.6240 2.2480 2.4370 detection rate(0.01) 0.7478 0.5166 0.7178 0.7182 0.8265 0.8145 distance to sample mean 284.1000 335.4000 266.7000 298.7000 212.2000 282.8000 HP27 HP75 A190N A4N A190P A4P mean 8.5520 8.1660 8.4600 8.1760 8.0330 8.5530 standard deviation 2.5050 2.4220 2.7490 2.9450 2.4510 2.9110 detection rate(0.01) 0.6902 0.6741 0.5803 0.4607 0.6253 0.5407 distance to sample mean 243.8000 252.8000 299.3000 352.6000 263.0000 353.8000 A10P KT65N KT50N KT01N KT27N KT65P mean 9.7460 9.4720 8.5610 9.3940 8.4880 8.1720 standard deviation 2.4930 2.6780 2.7550 2.2790 2.7980 2.8650 detection rate(0.01) 0.7805 0.7237 0.6034 0.8054 0.5725 0.5004 distance to sample mean 338.7000 338.3000 317.2000 233.3000 316.2000 350.8000 KT50P KT01P KT27P mean 8.5120 8.1190 8.6020 standard deviation 2.7240 2.4180 2.4280 detection rate(0.01) 0.5722 0.6046 0.6863 distance to sample mean 305.1000 246.4000 232.5000 Major Operation History: submitted finished 1 2010-05-21 12:28:46 2010-05-21 12:29:12 2 2010-05-21 12:29:12 2010-05-21 12:29:13 command 1 lumiR("raw_data_lumi_21.txt", convertNuID = FALSE) 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) lumiVersion 1 1.14.0 2 1.14.0 > lumi.T <- lumiT(katie.lumi) Perform vst transformation ... No Standard Deviation correction was applied becasue of missing bead number information. 2010-05-21 12:31:05 , processing array 1 2010-05-21 12:31:06 , processing array 2 2010-05-21 12:31:06 , processing array 3 2010-05-21 12:31:06 , processing array 4 2010-05-21 12:31:06 , processing array 5 2010-05-21 12:31:06 , processing array 6 2010-05-21 12:31:06 , processing array 7 2010-05-21 12:31:06 , processing array 8 2010-05-21 12:31:06 , processing array 9 2010-05-21 12:31:06 , processing array 10 2010-05-21 12:31:07 , processing array 11 2010-05-21 12:31:07 , processing array 12 2010-05-21 12:31:07 , processing array 13 2010-05-21 12:31:07 , processing array 14 2010-05-21 12:31:07 , processing array 15 2010-05-21 12:31:07 , processing array 16 2010-05-21 12:31:07 , processing array 17 2010-05-21 12:31:08 , processing array 18 2010-05-21 12:31:08 , processing array 19 2010-05-21 12:31:08 , processing array 20 2010-05-21 12:31:08 , processing array 21 > lumi.N <- lumiN(lumi.T) Perform quantile normalization ... > lumi.N.Q <- lumiQ(lumi.N) Perform Quality Control assessment of the LumiBatch object ... > summary(lumi.N.Q, 'QC') Data dimension: 24526 genes x 21 samples Summary of Samples: NC37 NC54 NC2 NC5 HP13 HP3 mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660 standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660 detection rate(0.01) 0.7478 0.5166 0.7178 0.7182 0.8265 0.8145 distance to sample mean 204.5000 221.7000 186.4000 198.6000 153.3000 168.0000 HP27 HP75 A190N A4N A190P A4P mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660 standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660 detection rate(0.01) 0.6902 0.6741 0.5803 0.4607 0.6253 0.5407 distance to sample mean 181.1000 192.1000 203.0000 232.5000 190.6000 233.2000 A10P KT65N KT50N KT01N KT27N KT65P mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660 standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660 detection rate(0.01) 0.7805 0.7237 0.6034 0.8054 0.5725 0.5004 distance to sample mean 215.5000 218.1000 216.5000 163.1000 214.3000 236.7000 KT50P KT01P KT27P mean 9.1660 9.1660 9.1660 standard deviation 1.9660 1.9660 1.9660 detection rate(0.01) 0.5722 0.6046 0.6863 distance to sample mean 211.7000 186.3000 175.6000 Major Operation History: submitted finished 1 2010-05-21 12:28:46 2010-05-21 12:29:12 2 2010-05-21 12:29:12 2010-05-21 12:29:13 3 2010-05-21 12:30:14 2010-05-21 12:30:19 4 2010-05-21 12:30:14 2010-05-21 12:30:19 5 2010-05-21 12:30:14 2010-05-21 12:30:19 6 2010-05-21 12:31:04 2010-05-21 12:31:08 7 2010-05-21 12:31:19 2010-05-21 12:31:19 8 2010-05-21 12:31:28 2010-05-21 12:31:28 command 1 lumiR("raw_data_lumi_21.txt", convertNuID = FALSE) 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) 3 addNuID2lumi(x.lumi = katie.lumi, annotationFile = "HUMANREF- 8_V3_0_R1_11282963_A_WGDASL", 4 annotationColName = c(sequence = "Probe_Sequence", probe = "Probe_Id", 5 symbol = "Symbol")) 6 lumiT(x.lumi = katie.lumi) 7 lumiN(x.lumi = lumi.T) 8 lumiQ(x.lumi = lumi.N) lumiVersion 1 1.14.0 2 1.14.0 3 1.14.0 4 1.14.0 5 1.14.0 6 1.14.0 7 1.14.0 8 1.14.0 > write.exprs(lumi.N.Q, file='normkatieData21anno.txt') > sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_1.14.0 MASS_7.3-5 RSQLite_0.8-4 [4] DBI_0.2-5 preprocessCore_1.10.0 mgcv_1.6-1 [7] affy_1.26.0 annotate_1.26.0 AnnotationDbi_1.10.0 [10] Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 grid_2.11.0 lattice_0.18-5 Matrix_0.999375-38 [5] nlme_3.1-96 tools_2.11.0 xtable_1.5-6 > I hope someone can help me with this. Thank you in advance. Katie

Hi, Katie Just reminder, in the following scripts, you type filename, not fileName in lumiR function. >> fileName <- 'raw_data_lumi_21.txt' >> katie.lumi = lumiR(filename, sampleInfoFile='sample_table_21.txt', >> convertNuID=FALSE) > Error in file.exists(fileName) : object 'filename' not found One easy way is to follow the instruction in lumi vignette and you can use lookUp function to map nuIDs to any other IDs in lumiHumanAll.db . Gilbert On 5/21/10 6:43 AM, "Taylor, Katie" <kt70 at="" leicester.ac.uk=""> wrote: > Hi, > > I am trying to annotate my illumina microarray using the following script that > I found online. However, I am having some difficulties with it as it is not > writing out the annotation data with the normalised data. Also, using this > script means that I don't know how to load in the sample file info. I have > copied the script that I used and the R output and session info below. Any > help would be greatly appreciated. > > > Script: > >> library(lumi) >> fileName <- 'raw_data_lumi_21.txt' >> katie.lumi = lumiR(fileName, convertNuID=FALSE) >> katie.lumi = addNuID2lumi(katie.lumi, > + annotationFile='HUMANREF-8_V3_0_R1_11282963_A_WGDASL', > + annotationColName=c(sequence='Probe_Sequence', probe='Probe_Id', > symbol='Symbol')) >> katie.lumi >> summary(katie.lumi, 'QC') >> lumi.T <- lumiT(katie.lumi) >> lumi.N <- lumiN(lumi.T) >> lumi.N.Q <- lumiQ(lumi.N) >> summary(lumi.N.Q, 'QC') >> write.exprs(lumi.N.Q, file='normkatieData21anno.txt') > > > R output: > >> library(lumi) > Loading required package: annotate > Loading required package: AnnotationDbi > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affy > Loading required package: mgcv > This is mgcv 1.6-1. For overview type `help("mgcv-package")'. > Loading required package: preprocessCore > Loading required package: RSQLite > Loading required package: DBI > Loading required package: MASS >> fileName <- 'raw_data_lumi_21.txt' >> katie.lumi = lumiR(filename, sampleInfoFile='sample_table_21.txt', >> convertNuID=FALSE) > Error in file.exists(fileName) : object 'filename' not found >> katie.lumi = lumiR(fileName, sampleInfoFile='sample_table_21.txt', >> convertNuID=FALSE) > Error in read.table(file = fileName, header = TRUE, sep = sep, dec = dec, : > unused argument(s) (sampleInfoFile = "sample_table_21.txt") >> katie.lumi = lumiR(fileName, convertNuID=FALSE) > Perform Quality Control assessment of the LumiBatch object ... >> katie.lumi = addNuID2lumi(katie.lumi, > + annotationFile='HUMANREF-8_V3_0_R1_11282963_A_WGDASL', > + annotationColName=c(sequence='Probe_Sequence', probe='Probe_Id', > symbol='Symbol')) > Directly converting probe sequence to nuIDs ... >> katie.lumi > Summary of data information: > Data File Information: > > > Major Operation History: > submitted finished > 1 2010-05-21 12:28:46 2010-05-21 12:29:12 > 2 2010-05-21 12:29:12 2010-05-21 12:29:13 > 3 2010-05-21 12:30:14 2010-05-21 12:30:19 > 4 2010-05-21 12:30:14 2010-05-21 12:30:19 > 5 2010-05-21 12:30:14 2010-05-21 12:30:19 > > command > 1 lumiR("raw_data_lumi_21.txt", > convertNuID = FALSE) > 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, > verbose = verbose) > 3 addNuID2lumi(x.lumi = katie.lumi, annotationFile = > "HUMANREF-8_V3_0_R1_11282963_A_WGDASL", > 4 annotationColName = c(sequence = "Probe_Sequence", probe > = "Probe_Id", > 5 > symbol = "Symbol")) > lumiVersion > 1 1.14.0 > 2 1.14.0 > 3 1.14.0 > 4 1.14.0 > 5 1.14.0 > > Object Information: > LumiBatch (storageMode: lockedEnvironment) > assayData: 24526 features, 21 samples > element names: detection, exprs, se.exprs > protocolData: none > phenoData > sampleNames: NC37, NC54, ..., KT27P (21 total) > varLabels and varMetadata description: > sampleID: The unique Illumina microarray Id > featureData > featureNames: Ku8QhfS0n_hIOABXuE, fqPEquJRRlSVSfL.8A, ..., > N8t5EuJCr0Tk9.zHno (24526 total) > fvarLabels and fvarMetadata description: > ProbeID: The Illumina microarray identifier > TargetID: The Illumina TargetID > ...: ... > PROBE_COORDINATES: PROBE_COORDINATES > (8 total) > experimentData: use 'experimentData(object)' > Annotation: lumiHumanAll.db > Control Data: Available > QC information: Please run summary(x, 'QC') for details! >> summary(katie.lumi, 'QC') > Data dimension: 24526 genes x 21 samples > > Summary of Samples: > NC37 NC54 NC2 NC5 HP13 HP3 > mean 8.8950 7.8930 8.8250 9.0190 9.3190 9.6140 > standard deviation 2.5030 2.7780 2.5320 2.6240 2.2480 2.4370 > detection rate(0.01) 0.7478 0.5166 0.7178 0.7182 0.8265 0.8145 > distance to sample mean 284.1000 335.4000 266.7000 298.7000 212.2000 282.8000 > HP27 HP75 A190N A4N A190P A4P > mean 8.5520 8.1660 8.4600 8.1760 8.0330 8.5530 > standard deviation 2.5050 2.4220 2.7490 2.9450 2.4510 2.9110 > detection rate(0.01) 0.6902 0.6741 0.5803 0.4607 0.6253 0.5407 > distance to sample mean 243.8000 252.8000 299.3000 352.6000 263.0000 353.8000 > A10P KT65N KT50N KT01N KT27N KT65P > mean 9.7460 9.4720 8.5610 9.3940 8.4880 8.1720 > standard deviation 2.4930 2.6780 2.7550 2.2790 2.7980 2.8650 > detection rate(0.01) 0.7805 0.7237 0.6034 0.8054 0.5725 0.5004 > distance to sample mean 338.7000 338.3000 317.2000 233.3000 316.2000 350.8000 > KT50P KT01P KT27P > mean 8.5120 8.1190 8.6020 > standard deviation 2.7240 2.4180 2.4280 > detection rate(0.01) 0.5722 0.6046 0.6863 > distance to sample mean 305.1000 246.4000 232.5000 > > Major Operation History: > submitted finished > 1 2010-05-21 12:28:46 2010-05-21 12:29:12 > 2 2010-05-21 12:29:12 2010-05-21 12:29:13 > command > 1 lumiR("raw_data_lumi_21.txt", convertNuID = FALSE) > 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) > lumiVersion > 1 1.14.0 > 2 1.14.0 >> lumi.T <- lumiT(katie.lumi) > Perform vst transformation ... > No Standard Deviation correction was applied becasue of missing bead number > information. > 2010-05-21 12:31:05 , processing array 1 > 2010-05-21 12:31:06 , processing array 2 > 2010-05-21 12:31:06 , processing array 3 > 2010-05-21 12:31:06 , processing array 4 > 2010-05-21 12:31:06 , processing array 5 > 2010-05-21 12:31:06 , processing array 6 > 2010-05-21 12:31:06 , processing array 7 > 2010-05-21 12:31:06 , processing array 8 > 2010-05-21 12:31:06 , processing array 9 > 2010-05-21 12:31:06 , processing array 10 > 2010-05-21 12:31:07 , processing array 11 > 2010-05-21 12:31:07 , processing array 12 > 2010-05-21 12:31:07 , processing array 13 > 2010-05-21 12:31:07 , processing array 14 > 2010-05-21 12:31:07 , processing array 15 > 2010-05-21 12:31:07 , processing array 16 > 2010-05-21 12:31:07 , processing array 17 > 2010-05-21 12:31:08 , processing array 18 > 2010-05-21 12:31:08 , processing array 19 > 2010-05-21 12:31:08 , processing array 20 > 2010-05-21 12:31:08 , processing array 21 >> lumi.N <- lumiN(lumi.T) > Perform quantile normalization ... >> lumi.N.Q <- lumiQ(lumi.N) > Perform Quality Control assessment of the LumiBatch object ... >> summary(lumi.N.Q, 'QC') > Data dimension: 24526 genes x 21 samples > > Summary of Samples: > NC37 NC54 NC2 NC5 HP13 HP3 > mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660 > standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660 > detection rate(0.01) 0.7478 0.5166 0.7178 0.7182 0.8265 0.8145 > distance to sample mean 204.5000 221.7000 186.4000 198.6000 153.3000 168.0000 > HP27 HP75 A190N A4N A190P A4P > mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660 > standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660 > detection rate(0.01) 0.6902 0.6741 0.5803 0.4607 0.6253 0.5407 > distance to sample mean 181.1000 192.1000 203.0000 232.5000 190.6000 233.2000 > A10P KT65N KT50N KT01N KT27N KT65P > mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660 > standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660 > detection rate(0.01) 0.7805 0.7237 0.6034 0.8054 0.5725 0.5004 > distance to sample mean 215.5000 218.1000 216.5000 163.1000 214.3000 236.7000 > KT50P KT01P KT27P > mean 9.1660 9.1660 9.1660 > standard deviation 1.9660 1.9660 1.9660 > detection rate(0.01) 0.5722 0.6046 0.6863 > distance to sample mean 211.7000 186.3000 175.6000 > > Major Operation History: > submitted finished > 1 2010-05-21 12:28:46 2010-05-21 12:29:12 > 2 2010-05-21 12:29:12 2010-05-21 12:29:13 > 3 2010-05-21 12:30:14 2010-05-21 12:30:19 > 4 2010-05-21 12:30:14 2010-05-21 12:30:19 > 5 2010-05-21 12:30:14 2010-05-21 12:30:19 > 6 2010-05-21 12:31:04 2010-05-21 12:31:08 > 7 2010-05-21 12:31:19 2010-05-21 12:31:19 > 8 2010-05-21 12:31:28 2010-05-21 12:31:28 > > command > 1 lumiR("raw_data_lumi_21.txt", > convertNuID = FALSE) > 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, > verbose = verbose) > 3 addNuID2lumi(x.lumi = katie.lumi, annotationFile = > "HUMANREF-8_V3_0_R1_11282963_A_WGDASL", > 4 annotationColName = c(sequence = "Probe_Sequence", probe > = "Probe_Id", > 5 > symbol = "Symbol")) > 6 > lumiT(x.lumi = katie.lumi) > 7 > lumiN(x.lumi = lumi.T) > 8 > lumiQ(x.lumi = lumi.N) > lumiVersion > 1 1.14.0 > 2 1.14.0 > 3 1.14.0 > 4 1.14.0 > 5 1.14.0 > 6 1.14.0 > 7 1.14.0 > 8 1.14.0 >> write.exprs(lumi.N.Q, file='normkatieData21anno.txt') >> sessionInfo() > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_1.14.0 MASS_7.3-5 RSQLite_0.8-4 > [4] DBI_0.2-5 preprocessCore_1.10.0 mgcv_1.6-1 > [7] affy_1.26.0 annotate_1.26.0 AnnotationDbi_1.10.0 > [10] Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 grid_2.11.0 lattice_0.18-5 > Matrix_0.999375-38 > [5] nlme_3.1-96 tools_2.11.0 xtable_1.5-6 >> > > > I hope someone can help me with this. Thank you in advance. > > Katie > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi, I was trying to use beadarray package to process bead-level data from mouse refV2 illumina single-color beadarray. According to the manual, I first read in the background-subtracted data directly from csv data and then generate beadsummary data. However, the boxplot of log2 of beadsummary data looks almost the same as the un-logged background-subtracted bead-level data. I was very confused about it and hope someone could point out the possible reasons. I have attached the boxplot of un-logged background- substracted bead-level data, log2 bead-summary data and un-logged bead-summary data. I also pasted the script and sessionInfo. Thank you very much. Best, Yiwen """ library(beadarray) targets=read.table("targets.txt",sep="\t",header=TRUE,as.is=TRUE) BLData=readIllumina(arrayNames=targets$ArrayName,textType=".csv",targe ts=targets,useImages=FALSE,backgroundMethod="none",annoPkg="Mousev2") BSData=createBeadSummaryData(BLData,imagesPerArray=1) par(mfrow=c(1,3),mai=c(2,0.5,0.2,0.1)) boxplotBeads(BLData,las=2,outline=FALSE,ylim=c(4,8),main="Background Corrected") boxplot(as.data.frame(log2(exprs(BSData))),outline=FALSE,ylim=c(4,8),y lab="log2(intensity)",main="Bead summary data") boxplot(as.data.frame(exprs(BSData)),outline=FALSE,ylim=c(16,64),ylab= "log2(intensity)",main="Bead summary data") > sessionInfo() R version 2.9.0 (2009-04-17) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_1.12.1 hwriter_1.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] limma_2.18.0 tools_2.9.0 """ -------------- next part -------------- A non-text attachment was scrubbed... Name: bead-data0521.pdf Type: application/pdf Size: 282580 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100521="" 647b55f9="" attachment.pdf="">