[BioC] Making three-way and four-way comparisons
Ryan C. Thompson
rct at thompsonclan.org
Thu Apr 10 20:05:53 CEST 2014
Are you looking for genes that have any difference at all between any of
the three populations, or are you looking specifically for genes that
are different in *both* the A vs B and A vs C comparisons? For the
former case, you can pass multiple coefficients or contrasts to the
testing functions (glmLRT or glmQLFTest) to perform an ANOVA-like test.
For the latter, you should probably adapt the approach recommended by
Grodon Smyth in a recent thread on this list[1]. Specifically, perform
each test separately and take the intersection of significant genes.
-Ryan
[1] https://stat.ethz.ch/pipermail/bioconductor/2014-April/058822.html
On 04/10/2014 07:31 AM, Maria [guest] wrote:
> 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?
>
> Regards,
> Maria
>
> -- output of sessionInfo():
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor
mailing list