[BioC] Limma: how to extract mean of groups?

[Hooiveld, Guido]

Hi James,

Thanks. I indeed had seen that before, but I had the impression the
'coefficients' actually are the log2 of the fold change...?!?
Anywayz, I'll have a closer look at it to make sure I understand it
correctly.

Best,
Guido


 

> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: 06 July 2009 18:50
> To: Hooiveld, Guido
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Limma: how to extract mean of groups?
> 
> Hi Guido,
> 
> Hooiveld, Guido wrote:
> > Dear list,
> >  
> > Is it possible to extract the group means + SD from Limma's output?
> >  
> > I do know that the "Amean" can be extracted (fit2$Amean), 
> but this is 
> > the mean across all arrays/groups, and i am also interested in the 
> > means of the experimental groups.
> 
> Have you read the relevant help page (hint ?MArrayLM-class)?
> 
> I get
> 
> Slots/Components:
> 
>       'MArrayLM' objects do not contain any slots (apart from '.Data')
>       but they should contain the following list components:
> 
>       'coefficients': 'matrix' containing fitted coefficients or
>            contrasts
> 
>       'stdev.unscaled': 'matrix' containing unscaled standard 
> deviations
>            of the coefficients or contrasts
> 
> Which appears to be what you want.
> 
> Best,
> 
> Jim
> 
> 
> > Therefore, is it somehow possible to extact the mean (+ SD) of the 
> > groups that are defined by the contrast matrix? Thus in my 
> particular 
> > case the mean + SD of the WT.Con, WT.WY. KO.Con and KO.WY groups.
> >  
> > Thanks,
> > Guido
> >  
> >  
> > library(affy)
> > library(limma)
> >  
> > targets <- readTargets("targets.txt")
> > data <- ReadAffy(filenames=targets$FileName)
> > x.norm <- rma(data)
> > 
> > TS <- paste(targets$Strain, targets$Treatment, sep=".") TS <- 
> > factor(TS, levels=c("WT.Con","WT.WY","KO.Con","KO.WY"))
> > design <- model.matrix(~0+TS)
> > colnames(design) <- levels(TS)
> > fit <- lmFit(eset, design)
> > cont.matrix <- makeContrasts(WTwyvWTc=WT.WY-WT.Con,
> > KOwyvKOc=KO.WY-KO.Con, levels=design)
> > fit2 <- contrasts.fit(fit, cont.matrix)
> > fit2 <- eBayes(fit2)
> > 
> > ------------------------------------------------
> > Guido Hooiveld, PhD
> > Nutrition, Metabolism & Genomics Group Division of Human Nutrition 
> > Wageningen University Biotechnion, Bomenweg 2
> > NL-6703 HD Wageningen
> > the Netherlands
> > tel: (+)31 317 485788
> > fax: (+)31 317 483342 
> > internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
> > email:      guido.hooiveld at wur.nl 
> > 
> > 
> > 
> > 	[[alternative HTML version deleted]]
> > 
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> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
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> 734-615-7826
> 
>