[BioC] edgeR

[Jahn Davik]

Great! Thank you.
That worked well.
An additional one: Can you in this framework filter out the DE transcripts with a particular direction? E.g., if I wanted only the one with higher counts in one of the elements from lrt1? I have done that using the logFC (and exact tests), but I am not able to see how this can be done here.

jahn

-----Opprinnelig melding-----
Fra: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sendt: 8. april 2014 02:22
Til: Jahn Davik
Kopi: Bioconductor mailing list
Emne: edgeR

If you want to select transcript that are DE for one contrast but not another, first test each contrast:

   lrt1 <- glmLRT(fit, contrast=mycontrast1)
   lrt2 <- glmLRT(fit, contrast=mycontrast2)

Then apply significance thresholds:

   dt1 <- decideTestsDGE(lrt1)
   dt2 <- decideTestsDGE(lrt2)

Then select the transcripts you want:

   selected <- !dt1 & dt2

Best wishes
Gordon


> Date: Sun,  6 Apr 2014 03:32:49 -0700 (PDT)
> From: "Jahn Davik [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, jahn.davik at bioforsk.no
> Subject: [BioC] edgeR
>
>
> 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 ?
>
> regards
> JD

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