[BioC] Testing main effects and interactions in edgeR without contrasts

[James W. MacDonald]

Hi David,

You can always use voom() (in edgeR) and then analyze the data using 
limma.

Best,

Jim



On Friday, December 13, 2013 5:25:36 AM, David Shuker [guest] wrote:
>
> Dear friends,
>
> We are very interested in testing main effects and interactions for a 2x3 factorial RNA-seq project we have been running (we have reasonable replication: 7 biological replicates per treatment combination, i.e. 42 libraries in total).
>
> >From our reading of the edgeR Users guide and various posts on-line, it looks as though the package is set-up to test effects via contrasts. Although a contrasts-approach allows the testing of differences between specific treatment combinations, we would like to test interactions and main effects in a more traditional glm/anova format. (We note that testing whether the two contrasts associated with a three-level main effect - a, b, c - are significant is not the same question as testing whether the main effect itself is significant, or of course vice versa.)
>
> We would like outputs and tests along the lines of glm() or anova(), not "anova-like" tests that use the results of one or more contrasts to ask similar, but not exactly the same, questions of the data.
>
> We apologise in advance if we have either missed something obvious in the user guide or relevant discussion somewhere online. If edgeR does not have this functionality, we will probably use edgeR in conjunction with other packages.
>
> As with all the community, we remain in awe of the work the edgeR developers have done, and thank them in advance.
>
> Best wishes,
>
> Dave Shuker
>
>   -- output of sessionInfo():
>
> NA
>
> --
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099