[BioC] Making three-way and four-way comparisons

Maria [guest] guest at bioconductor.org
Thu Apr 10 16:31:13 CEST 2014

Hi all,
I have read the entire edgeR user guide and some posts on here but I still do not understand if it possible to make non-pairwise contrasts in edgeR (or is it even an oxymoron)in the GLM mode. The only non-simple contrasts I could find are of the form (taken from the user guide):
DrugvsPlacebo.2h = (Drug.2h-Drug.0h)-(Placebo.2h-Placebo.0h)
but I have different setup.

I have 3 different populations and I would like to see find genes that are significantly different between population A and B, and A and C simultaneously.
Of course, I could make pairwise comparisons and look for intercept in DEG, but I am not sure it is the proper way?


 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] edgeR_3.2.4             limma_3.16.8            DESeq2_1.0.19           RcppArmadillo_0.4.200.0
 [5] Rcpp_0.11.1             GenomicRanges_1.12.5    IRanges_1.18.4          pasilla_0.2.16         
 [9] DESeq_1.12.1            lattice_0.20-29         locfit_1.5-9.1          DEXSeq_1.6.0           
[13] Biobase_2.20.1          BiocGenerics_0.6.0      BiocInstaller_1.10.4   

loaded via a namespace (and not attached):
 [1] annotate_1.38.0      AnnotationDbi_1.22.6 biomaRt_2.16.0       Biostrings_2.28.0    bitops_1.0-6        
 [6] DBI_0.2-7            genefilter_1.42.0    geneplotter_1.38.0   grid_3.0.1           hwriter_1.3         
[11] RColorBrewer_1.0-5   RCurl_1.95-4.1       Rsamtools_1.12.4     RSQLite_0.11.4       statmod_1.4.18      
[16] stats4_3.0.1         stringr_0.6.2        survival_2.37-7      tools_3.0.1          XML_3.98-1.1        
[21] xtable_1.7-3         zlibbioc_1.6.0  

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