[BioC] edgeR

Jahn Davik [guest] guest at bioconductor.org
Sun Apr 6 12:32:49 CEST 2014

Hi there,
I have a question regarding edgeR - or it might actually be a more general statistical question. In any case, I am using edgeR to analyse my read counts and really would appreciate help.
My experimental setup is:
Two genotypes (B and S)
Two treatments ('trt' vs 'ntrt')
Two time points (0hs 8hs).
(Three bio reps)

Now, I would like to identify reads that are specific to either of the genotypes as their response to the treatment over the time points. 
I expect that I can do pairwise comparisons like:
'B_tr_0hs' vs 'B_trt_8hs'), and
'B_ntr_0hs' vs 'B_ntrt_8hs'), and continuing doing the same with the S-genotype. Subsequently, using a suitable tool, I could filter out the transcripts for, say, B's response to treatment over these two time points that are not found in B. It is, however, a little tedious so my question here is whether this can be modeled and extracted in edgeR's GLM ?


 -- output of sessionInfo(): 

not relevant

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list