Hi, I have just tried to load illumina microarray data into lumi and I added loadAnnotaion=TRUE. However, when I output the data to an .txt document, only the nuIDs are there and the annotation has gone. Does anyone know what i've done wrong? Also, I have 24 samples, with 6 groups. How do I perform comparisons between the groups using limma? Can I do all of the comparisons at once, producing different documents for each or is it better to do each comparison individually? I would appreciate your comments. I have copied the session info and R output for lumi below: R version 2.11.0 (2010-04-22) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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.batch(fileName, sampleInfoFile='sample_table_21.txt', inputAnnotation = TRUE) Inputting the data ... Adding nuID to the data ... Directly converting probe sequence to nuIDs ... Perform Quality Control assessment of the LumiBatch object ... > katie.lumi Summary of data information: Data File Information: Major Operation History: submitted finished 1 2010-05-20 14:00:37 2010-05-20 14:01:08 2 2010-05-20 14:00:37 2010-05-20 14:01:08 3 2010-05-20 14:01:08 2010-05-20 14:01:08 command 1 lumiR.batch("raw_data_lumi_21.txt", 2 inputAnnotation = TRUE) 3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) lumiVersion 1 1.14.0 2 1.14.0 3 1.14.0 Object Information: LumiBatch (storageMode: lockedEnvironment) assayData: 24526 features, 21 samples element names: detection, exprs, se.exprs protocolData: none phenoData rowNames: NC37, NC54, ..., KT27P (21 total) varLabels and varMetadata description: Index: NA sampleID: NA ...: ... Noise: NA (22 total) 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 2010-05-20 14:00:37 2010-05-20 14:01:08 2 2010-05-20 14:00:37 2010-05-20 14:01:08 3 2010-05-20 14:01:08 2010-05-20 14:01:08 command 1 lumiR.batch("raw_data_lumi_21.txt", 2 inputAnnotation = TRUE) 3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) lumiVersion 1 1.14.0 2 1.14.0 3 1.14.0 > pdf("plots.pdf") > plot(katie.lumi, what='density') > density(katie.lumi) > plotCDF(katie.lumi, reverse=TRUE) > plot(katie.lumi, what='pair') > pairs(katie.lumi, smoothScatter=T) KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 > MAplot(katie.lumi, smoothScatter=TRUE) > plot(katie.lumi, what='cv') > plot(katie.lumi, what='boxplot') > lumi.T <- lumiT(katie.lumi) Perform vst transformation ... No Standard Deviation correction was applied becasue of missing bead number information. 2010-05-20 14:16:47 , processing array 1 2010-05-20 14:16:47 , processing array 2 2010-05-20 14:16:47 , processing array 3 2010-05-20 14:16:47 , processing array 4 2010-05-20 14:16:47 , processing array 5 2010-05-20 14:16:47 , processing array 6 2010-05-20 14:16:47 , processing array 7 2010-05-20 14:16:47 , processing array 8 2010-05-20 14:16:47 , processing array 9 2010-05-20 14:16:48 , processing array 10 2010-05-20 14:16:48 , processing array 11 2010-05-20 14:16:48 , processing array 12 2010-05-20 14:16:48 , processing array 13 2010-05-20 14:16:48 , processing array 14 2010-05-20 14:16:48 , processing array 15 2010-05-20 14:16:48 , processing array 16 2010-05-20 14:16:48 , processing array 17 2010-05-20 14:16:49 , processing array 18 2010-05-20 14:16:49 , processing array 19 2010-05-20 14:16:49 , processing array 20 2010-05-20 14:16:49 , processing array 21 > trans <- plotVST(lumi.T) > dev.off() null device 1 > pdf(plots_norm.pdf) Error in gsub("%%", "", s) : object 'plots_norm.pdf' not found > pdf("plots_norm.pdf") > 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 2010-05-20 14:00:37 2010-05-20 14:01:08 2 2010-05-20 14:00:37 2010-05-20 14:01:08 3 2010-05-20 14:01:08 2010-05-20 14:01:08 4 2010-05-20 14:16:45 2010-05-20 14:16:49 5 2010-05-20 14:17:52 2010-05-20 14:17:53 6 2010-05-20 14:18:02 2010-05-20 14:18:02 command 1 lumiR.batch("raw_data_lumi_21.txt", 2 inputAnnotation = TRUE) 3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) 4 lumiT(x.lumi = katie.lumi) 5 lumiN(x.lumi = lumi.T) 6 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 > plot(lumi.N.Q, what='density') > plot(lumi.N.Q, what='boxplot') > > plot(lumi.N.Q, what='pair') > plot(lumi.N.Q, what='MAplot') > write.exprs(lumi.N.Q, file='normkatieData21_ann.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 KernSmooth_2.23-3 lattice_0.18-5 [5] Matrix_0.999375-38 nlme_3.1-96 tools_2.11.0 xtable_1.5-6 > Best Wishes, Katie

Hi, Katie When you set inputAnnotation to TRUE, you have to specify annotationColumn. The lumi.R manual page states :" they can set the parameter "inputAnnotation" as TRUE. At the same time, they can also specify which columns to be inputted by setting parameter "annotationColumn"." You can use lumiHumanAll.db to map nuIDs in your lumi object to any other IDs. Gilbert On 5/20/10 8:25 AM, "Taylor, Katie" <kt70 at="" leicester.ac.uk=""> wrote: > Hi, > > I have just tried to load illumina microarray data into lumi and I added > loadAnnotaion=TRUE. However, when I output the data to an .txt document, only > the nuIDs are there and the annotation has gone. Does anyone know what i've > done wrong? > > Also, I have 24 samples, with 6 groups. How do I perform comparisons between > the groups using limma? Can I do all of the comparisons at once, producing > different documents for each or is it better to do each comparison > individually? I would appreciate your comments. > > I have copied the session info and R output for lumi below: > > R version 2.11.0 (2010-04-22) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> 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.batch(fileName, sampleInfoFile='sample_table_21.txt', >> inputAnnotation = TRUE) > Inputting the data ... > > Adding nuID to the data ... > Directly converting probe sequence to nuIDs ... > Perform Quality Control assessment of the LumiBatch object ... >> katie.lumi > Summary of data information: > Data File Information: > > > Major Operation History: > submitted finished > 1 2010-05-20 14:00:37 2010-05-20 14:01:08 > 2 2010-05-20 14:00:37 2010-05-20 14:01:08 > 3 2010-05-20 14:01:08 2010-05-20 14:01:08 > command > 1 lumiR.batch("raw_data_lumi_21.txt", > 2 inputAnnotation = TRUE) > 3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) > lumiVersion > 1 1.14.0 > 2 1.14.0 > 3 1.14.0 > > Object Information: > LumiBatch (storageMode: lockedEnvironment) > assayData: 24526 features, 21 samples > element names: detection, exprs, se.exprs > protocolData: none > phenoData > rowNames: NC37, NC54, ..., KT27P (21 total) > varLabels and varMetadata description: > Index: NA > sampleID: NA > ...: ... > Noise: NA > (22 total) > 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 2010-05-20 14:00:37 2010-05-20 14:01:08 > 2 2010-05-20 14:00:37 2010-05-20 14:01:08 > 3 2010-05-20 14:01:08 2010-05-20 14:01:08 > command > 1 lumiR.batch("raw_data_lumi_21.txt", > 2 inputAnnotation = TRUE) > 3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) > lumiVersion > 1 1.14.0 > 2 1.14.0 > 3 1.14.0 >> pdf("plots.pdf") >> plot(katie.lumi, what='density') >> density(katie.lumi) >> plotCDF(katie.lumi, reverse=TRUE) >> plot(katie.lumi, what='pair') >> pairs(katie.lumi, smoothScatter=T) > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 >> MAplot(katie.lumi, smoothScatter=TRUE) >> plot(katie.lumi, what='cv') >> plot(katie.lumi, what='boxplot') >> lumi.T <- lumiT(katie.lumi) > Perform vst transformation ... > No Standard Deviation correction was applied becasue of missing bead number > information. > 2010-05-20 14:16:47 , processing array 1 > 2010-05-20 14:16:47 , processing array 2 > 2010-05-20 14:16:47 , processing array 3 > 2010-05-20 14:16:47 , processing array 4 > 2010-05-20 14:16:47 , processing array 5 > 2010-05-20 14:16:47 , processing array 6 > 2010-05-20 14:16:47 , processing array 7 > 2010-05-20 14:16:47 , processing array 8 > 2010-05-20 14:16:47 , processing array 9 > 2010-05-20 14:16:48 , processing array 10 > 2010-05-20 14:16:48 , processing array 11 > 2010-05-20 14:16:48 , processing array 12 > 2010-05-20 14:16:48 , processing array 13 > 2010-05-20 14:16:48 , processing array 14 > 2010-05-20 14:16:48 , processing array 15 > 2010-05-20 14:16:48 , processing array 16 > 2010-05-20 14:16:48 , processing array 17 > 2010-05-20 14:16:49 , processing array 18 > 2010-05-20 14:16:49 , processing array 19 > 2010-05-20 14:16:49 , processing array 20 > 2010-05-20 14:16:49 , processing array 21 >> trans <- plotVST(lumi.T) >> dev.off() > null device > 1 >> pdf(plots_norm.pdf) > Error in gsub("%%", "", s) : object 'plots_norm.pdf' not found >> pdf("plots_norm.pdf") >> 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 2010-05-20 14:00:37 2010-05-20 14:01:08 > 2 2010-05-20 14:00:37 2010-05-20 14:01:08 > 3 2010-05-20 14:01:08 2010-05-20 14:01:08 > 4 2010-05-20 14:16:45 2010-05-20 14:16:49 > 5 2010-05-20 14:17:52 2010-05-20 14:17:53 > 6 2010-05-20 14:18:02 2010-05-20 14:18:02 > command > 1 lumiR.batch("raw_data_lumi_21.txt", > 2 inputAnnotation = TRUE) > 3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose) > 4 lumiT(x.lumi = katie.lumi) > 5 lumiN(x.lumi = lumi.T) > 6 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 >> plot(lumi.N.Q, what='density') >> plot(lumi.N.Q, what='boxplot') >> >> plot(lumi.N.Q, what='pair') >> plot(lumi.N.Q, what='MAplot') >> write.exprs(lumi.N.Q, file='normkatieData21_ann.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 KernSmooth_2.23-3 lattice_0.18-5 > [5] Matrix_0.999375-38 nlme_3.1-96 tools_2.11.0 xtable_1.5-6 >> > > Best Wishes, > > 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 Katie The inputted annotation information is kept in the featureData slot. You can retrieve it using following command: annotation = pData(featureData(x.lumi)) # suppose x.lumi is the LumiBatch object keeping the data As for doing multiple comparison at the same time using limma, yes you can easily do it. But I suggest you read the tutorial of limma package. There are lots of good examples to follow. Pan On 5/21/10 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Message: 21 > Date: Thu, 20 May 2010 14:25:09 +0100 > From: "Taylor, Katie" <kt70 at="" leicester.ac.uk=""> > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] help with lumi > Message-ID: > <413DBF04CB18DC45AEC6B64AEA6F9B60304D72975D at EXC- MBX1.cfs.le.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I have just tried to load illumina microarray data into lumi and I added > loadAnnotaion=TRUE. However, when I output the data to an .txt document, only > the nuIDs are there and the annotation has gone. Does anyone know what i've > done wrong? > > Also, I have 24 samples, with 6 groups. How do I perform comparisons between > the groups using limma? Can I do all of the comparisons at once, producing > different documents for each or is it better to do each comparison > individually? I would appreciate your comments. > > I have copied the session info and R output for lumi below: >