[BioC] edgeR

Jahn Davik jahn.davik at bioforsk.no
Tue Apr 8 10:03:17 CEST 2014


Smashing!
Thanks.

jahn

-----Opprinnelig melding-----
Fra: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sendt: 8. april 2014 10:02
Til: Jahn Davik
Kopi: Bioconductor mailing list
Emne: Re: edgeR

Yes.  If you want transcripts that are up in contrast1 and down in
contrast2:

   selected <- (dt1>0) & (dt2<0)

Or up in contrast1 and not changing in contrast2:

   selected <- (dt1>0) & (dt2==0)

Gordon

On Tue, 8 Apr 2014, Jahn Davik wrote:

> 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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