[BioC] Link to picture: Comparison of diff. t-statistics, Limma and rowttests

[Boel Brynedal]

Hi, again,

Just a small note, the "fit3" in ordinary.t is simply a error from my
side. It should be:
ordinary.t <- fit$coef / fit$stdev.unscaled / fit$sigma 
This does not change the way ordinary.t behaves.

Best,
Boel

Thank you Al.

> 
> > -----Original Message-----
> > From: bioconductor-bounces at stat.math.ethz.ch 
> > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> > Boel Brynedal
> > Sent: 25 July 2008 12:19
> > To: bioconductor at stat.math.ethz.ch
> > Subject: [BioC] Link to picture: Comparison of diff. 
> > t-statistics, Limma and rowttests
> > 
> > 
> > Dear List,
> > 
> > Thank you (Wolfgang and Paolo) for telling me the attachment 
> > did not get through. This is a link to the picture: 
> > http://picasaweb.google.se/Boelbubblan/Statistics/photo
> > 
> > Cheers,
> > Boel
> > 
> > --~*~**~***~*~***~**~*~--
> > Boel Brynedal, MSc, PhD student
> > Karolinska  Institutet
> > Department of Clinical neuroscience
> > 
> > 
> > ----- Original Message -----
> > From: Boel Brynedal <Boel.Brynedal at ki.se>
> > Date: Friday, July 25, 2008 9:33 am
> > Subject: Comparison of diff. t-statistics, Limma and rowttests
> > To: bioconductor at stat.math.ethz.ch
> > 
> > > Dear List,
> > > 
> > > I have affy hgu133plus2 arrays from individuals with 
> > disease, in two 
> > > different stages of the disease. I've earlier used 
> > rowttests and FDR 
> > > correction. Now I was playing around with limma to see what 
> > I could do 
> > > (added different covariates etc) but also investigated the 
> > most simple 
> > > setting, comparing the two different stages directly using 
> > Limma. The 
> > > first thing that struck me was that limma "finds" only half 
> > the amount 
> > > of significantly diff expressed genes. So I started to look at 
> the 
> > > t-statistics from limma. Then I stumbled across this: when I do 
> a 
> > > qq-plot of the ordinary t-statistics they are far from normally 
> > > distributed, and actually totally strange. See attached 
> > plot comparing 
> > > the ordinary t, the moderate t (both from Limma) as well as t- 
> > > statisticsfrom rowttests ("Diff_tStatistics_Limma.jpg").
> > > 
> > > Am I doing something completely wrong? The assumption of equal
> > > variancetaken using ordinary t could not create this, could it? 
> > > Please help me
> > > figure out what's wrong here, I'm hoping I've done some stupid 
> > > mistake.What else could explain this? Thank you.
> > > 
> > > Best wishes,
> > > Boel
> > > 
> > > My code and sessionInfo:
> > > 
> > > # eset is a filtered, gcrma normalized ExpressionSet with ~10 000
> > > probesets, 24 arrays.
> > > library(limma)
> > > library(Biobase)
> > > library(genefilter)
> > > specific<-factor(c(rep("stageA",10),rep("stageB",14)),
> > > levels=c("stageB","stageA"))
> > > design<-model.matrix(~specific)
> > > fit<-lmFit(eset,design)
> > > Fit<-eBayes(fit)
> > > 
> > > ordinary.t <- fit3$coef / fit3$stdev.unscaled / fit3$sigma 
> > > moderate.t<-Fit$t[,2]
> > > rowttests.t<-rowttests(eset,fac=specific)
> > > 
> > > par(mfrow=c(1,3))
> > > qqnorm(ordinary.t,main="fit ordinary.t")
> > > qqnorm(moderate.t, main=" Fit moderate.t") 
> qqnorm(rowttests.t[,1], 
> > > main= "rowttests.t") 
> > > dev2bitmap("Diff_tStatistics_Limma.jpg",type="jpeg", height 
> > = 5, width 
> > > = 15, res = 75)
> > > 
> > > > sessionInfo()
> > > R version 2.7.1 (2008-06-23)
> > > x86_64-unknown-linux-gnu
> > > 
> > > locale:
> > > ...
> > > 
> > > attached base packages:
> > > [1] splines   tools     stats     graphics  grDevices utils     
> > > datasets[8] methods   base
> > > 
> > > other attached packages:
> > > [1] genefilter_1.20.0 survival_2.34-1   Biobase_2.0.1     
> > limma_2.14.5
> > > 
> > > loaded via a namespace (and not attached):
> > > [1] annotate_1.18.0     AnnotationDbi_1.2.2 DBI_0.2-4
> > > [4] RSQLite_0.6-9
> > > 
> > > --~*~**~***~*~***~**~*~--
> > > Boel Brynedal, MSc, PhD student
> > > Karolinska  Institutet
> > > Department of Clinical neuroscience
> > > 
> > >
> > 
> > _______________________________________________
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> > 
> 
> 
> 
> 
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