[BioC] help

[Michael Stapelberg]

Hi,

I hope someone can help me out.

I am using Bioconductor and limma to examine my microarrat data. What I  
am trying to do is eliminate any spots that have an NA between arrays  
before applying the design matrix in limma and applying the eBayes  
function. Even after I have  done this elimination process and have  
checked it, by having a look at the M values of the top genes in the  
topTable list, some of the genes still have an NA value for one array,  
but designated M values for the rest of the arrays in the group.

This is what I am typing into the workspace after normalisation and  
scalenormalisation:

A.object<-maA(objectscalenormalisation)
M.object<-maM(objectscalenormalisation)
Library(limma)
a<-is.na(M.object)
a<-apply(a,1,sum)
b[b==0]
which[b==0]
zero<-which(b==0)
x<- 
list(A=maA(objectscalenormalisation)[zero,],M=maM(objectscalenormalisati 
on)[zero,]
x.lmFit<-lmFit(x,c(1,-1,1,-1))
x.lmFit.Bayes<-eBayes(x.lmFit)
plot(x.lmFit.Bayes$coef,x.lmFit.Bayes$lods)
topTable(x.lmFit.Bayes,n=100)
On Wednesday, July 7, 2004, at 04:15  PM, James Wettenhall wrote:

Why might this not be working ?


Michael.
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