Question: Limma Ebayes on SILAC data
gravatar for reventropy2003
3 months ago by
reventropy20030 wrote:

Is there any need to set up a design or contrast matrix using limma ebayes on ratiometric replicates?  I have three replicate ratios that are log2 transformed.  I'm running ebayes:


data = read.csv(paste(inpath,fname,sep=""),header=T,stringsAsFactors=F,na.strings="NaN",sep="\t")

fit = lmFit(data[,c("rep1","rep2","rep3")]))
fit2 = eBayes(fit)
tt = topTable(fit2, adjust="BH",number=Inf,confint=T,'none')  


Where "rep 1-3" are the columns containing the ratio measurements.  Is this correct?  




ADD COMMENTlink modified 3 months ago by Gordon Smyth32k • written 3 months ago by reventropy20030
gravatar for Gordon Smyth
3 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

I am not familiar with SILAC ratiometric data but, if it produces log-expression ratios, then you could analyse the results like those from two colour microarrays. Your data appears to be similar to the design considered in Section 11.2.1 of the limma User's Guide. In that case, you don't need to create a design matrix -- the default linear model with just an intercept will do the job -- so your code seems correct.

ADD COMMENTlink written 3 months ago by Gordon Smyth32k
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