[BioC] limma - special case of contrasting

[Gordon K Smyth]

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
>

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