[BioC] p.adj and logFC

[James W. MacDonald]

Hi Yisong,

Yisong Zhen wrote:
> Hello All,
> I used the following script to find the genes that both have p.adj < 0.05
> and logFC < -1 in comparisons (TCdn - TCwt and Tcestw - TCwt).
> I checked one candidate gene in the normalized expression output
> (affy_My_data.txt). The first two are TCdn, middle two are TCwt and the last
> two are TCestw):
> 
> MKG.56.34.1_at  4.30886639379254 5.33637926862047 11.8385942887500
> 10.9736438003031 4.22713527087133 3.28741332008267
> 
> It seems that this gene have same logFC in two comparisons (TCdn~ TCwt and
> TCets~TCwt). But the p.adj is very different: one is 0.053759(TCdn~TCwt) and
> the other is 0.009286 (TCetsw~TCwt).
> 
> I am not familiar with LIMMA model and the code is simply from Biocoductor
> manual, please give some advice and tell me how to interpret this
> result.(How the p.adj is calculated? Why the same gene in two comparisons
> have same logFC but the p.adj is so different?)

The reason you get a different p-value with the same log FC is because 
the p-value is based on the t-statistic, not the fold change (although 
the fold change is the numerator of that statistic).

If you look at the t-statistics for these two genes you will see that 
they are different.

Best,

Jim


> 
> Thanks.
> 
> Yisong
> 
> 
> 
> library(limma)
> library(affy)
> targets<-readTargets("targets.txt")
> #targets;
> data<-ReadAffy(filenames=targets$FileName)
> eset<-rma(data)
> write.exprs(eset, file="affy_My_data.txt")
> design<-model.matrix(~-1+factor(c(1,1,2,2,3,3)))
> colnames(design)<-c("TCdn","TCwt","TCetsw")
> fit<-lmFit(eset,design)
> contrast.matrix<-makeContrasts(TCdn-TCwt,TCetsw-TCwt, levels=design)
> fit2<-contrasts.fit(fit, contrast.matrix)
> fit2<-eBayes(fit2)
> write.table(topTable(fit2, coef=1, adjust="fdr", sort.by="B", number=50000),
> file="limmadn_wt.xls", row.names=F, sep="\t")
> write.table(topTable(fit2, coef=2, adjust="fdr", sort.by="B", number=50000),
> file="limmaestw_wt.xls", row.names=F, sep="\t")
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662