[BioC] edgeR
Gordon K Smyth
smyth at wehi.EDU.AU
Tue Apr 8 02:22:27 CEST 2014
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
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}
More information about the Bioconductor
mailing list