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

[James W. MacDonald]

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 
> 
> 
> 
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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.
Ann Arbor MI 48109-5618
734-615-7826