Dear all! I'm trying to identify differentially expressed genes (DEGs) using limma with the following Targets file: CELfile donor treatmemt celltype file1 1 A C2 file2 1 B C2 file3 2 A C2 file4 2 B C2 file5 2 A C1 file6 2 B C1 file7 3 A C2 file8 3 B C2 file9 3 A C1 file10 3 B C1 file11 4 A C2 file12 4 B C2 file13 4 A C1 file14 4 B C1 file15 5 A C2 file16 5 B C2 file17 6 A C2 file18 6 B C2 file19 6 A C1 file20 6 B C1 file21 7 A C2 file22 7 B C2 file23 8 A C2 file24 8 B C2 file25 8 A C1 file26 8 B C1 file27 9 A C2 file28 9 B C2 file29 9 A C1 file30 9 B C1 file31 10 A C2 file32 10 B C2 I'd like to compare C1.A vs. (C1.B, C2.A, C2.B) while blocking the donors and get a list of DEGs. I'd greatly appreciate any ideas on how to approach this. Btw, I've already conducted C1.A vs. C1.B and C2.A vs. C2.B comparisons. Thanks, Mitja -- output of sessionInfo(): sessionInfo() R version 2.15.1 (2012-06-22) Platform: x8664-apple-darwin9.8.0/x8664 (64-bit) locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] statmod1.4.16 hgu133plus2cdf2.10.0 AnnotationDbi1.18.4 arrayQualityMetrics3.12.0 [5] limma3.12.3 affy1.34.0 Biobase2.16.0 BiocGenerics0.2.0 loaded via a namespace (and not attached): [1] affyio1.24.0 affyPLM1.32.0 annotate1.34.1 beadarray2.6.0 BeadDataPackR1.8.0 [6] BiocInstaller1.4.9 Biostrings2.24.1 Cairo1.5-2 cluster1.14.3 colorspace1.2-0 [11] DBI0.2-5 genefilter1.38.0 grid2.15.1 Hmisc3.10-1 hwriter1.3 [16] IRanges1.14.4 KernSmooth2.23-8 lattice0.20-10 latticeExtra0.6-24 plyr1.7.1 [21] preprocessCore1.18.0 RColorBrewer1.0-5 reshape21.2.1 RSQLite0.11.2 setRNG2011.11-2 [26] splines2.15.1 stats42.15.1 stringr0.6.1 survival2.36-14 SVGAnnotation0.93-1 [31] tools2.15.1 vsn3.24.0 XML3.95-0.1 xtable1.7-0 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.

Dear Mitja, I don't know what you mean by "compare C1.A vs. (C1.B, C2.A, C2.B)". What contrast, or what hypothesis, do you want to test exactly? Best wishes Gordon > Date: Fri, 7 Dec 2012 13:44:10 -0800 (PST) > From: "Mitrovic [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, mitmitrovic at gmail.com > Subject: [BioC] limma - special case of contrasting > > > Dear all! > > I'm trying to identify differentially expressed genes (DEGs) using limma with the following Targets file: > > CELfile donor treatmemt celltype > file1 1 A C2 > file2 1 B C2 > file3 2 A C2 > file4 2 B C2 > file5 2 A C1 > file6 2 B C1 > file7 3 A C2 > file8 3 B C2 > file9 3 A C1 > file10 3 B C1 > file11 4 A C2 > file12 4 B C2 > file13 4 A C1 > file14 4 B C1 > file15 5 A C2 > file16 5 B C2 > file17 6 A C2 > file18 6 B C2 > file19 6 A C1 > file20 6 B C1 > file21 7 A C2 > file22 7 B C2 > file23 8 A C2 > file24 8 B C2 > file25 8 A C1 > file26 8 B C1 > file27 9 A C2 > file28 9 B C2 > file29 9 A C1 > file30 9 B C1 > file31 10 A C2 > file32 10 B C2 > > I'd like to compare C1.A vs. (C1.B, C2.A, C2.B) while blocking the > donors and get a list of DEGs. I'd greatly appreciate any ideas on how > to approach this. Btw, I've already conducted C1.A vs. C1.B and C2.A vs. > C2.B comparisons. > > Thanks, > > Mitja > > -- output of sessionInfo(): > > sessionInfo() > > R version 2.15.1 (2012-06-22) Platform: x8664-apple- darwin9.8.0/x8664 (64-bit) > > locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8 > > attached base packages: [1] stats graphics grDevices utils datasets methods base > > other attached packages: [1] statmod1.4.16 hgu133plus2cdf2.10.0 AnnotationDbi1.18.4 arrayQualityMetrics3.12.0 [5] limma3.12.3 affy1.34.0 Biobase2.16.0 BiocGenerics0.2.0 > > loaded via a namespace (and not attached): [1] affyio1.24.0 affyPLM1.32.0 annotate1.34.1 beadarray2.6.0 BeadDataPackR1.8.0 > [6] BiocInstaller1.4.9 Biostrings2.24.1 Cairo1.5-2 cluster1.14.3 colorspace1.2-0 > [11] DBI0.2-5 genefilter1.38.0 grid2.15.1 Hmisc3.10-1 hwriter1.3 > [16] IRanges1.14.4 KernSmooth2.23-8 lattice0.20-10 latticeExtra0.6-24 plyr1.7.1 > [21] preprocessCore1.18.0 RColorBrewer1.0-5 reshape21.2.1 RSQLite0.11.2 setRNG2011.11-2 > [26] splines2.15.1 stats42.15.1 stringr0.6.1 survival2.36-14 SVGAnnotation0.93-1 [31] tools2.15.1 vsn3.24.0 XML3.95-0.1 xtable1.7-0 zlibbioc_1.2.0 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}