[BioC] limma - special case of contrasting

[Mitrovic [guest]]

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

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