[BioC] Filter genes on mas5calls

[Crispin Miller]

Hi,
You might also want to check out the functions:

detection.p.val, pairwise.comparison and pairwise.filter in the
developmental package 'simpleaffy'. They do the same thing, but in C, so
hopefully they're quite quick...

The package has only just been added, so fingers crossed ;-)

Cheers,

Crispin


> -----Original Message-----
> From: Ron Ophir [mailto:Lsophir at wisemail.weizmann.ac.il] 
> Sent: 08 December 2003 08:48
> To: bioconductor at stat.math.ethz.ch
> Subject: RE:[BioC] Filter genes on mas5calls
> 
> 
> Hi Anthony,
> I once wrote a script that takes AffyBatch as an input and 
> return detection calls. If it helps be my guest 
> DetectionCall<-function(AffyBatch,tau=0.015){
>  if (class(AffyBatch)!="AffyBatch") stop("Not AffyBatch object")
>  p<-numeric()
>  gn<-geneNames(AffyBatch) 
> for (g in gn){
>          
> r<-(pm(AffyBatch,g)-mm(AffyBatch,g))/(pm(AffyBatch,g)+mm(AffyB
> atch,g)) 
>           p<-rbind(p,apply(r,2,function
> (x){wilcox.test(x,mu=0.015,alt="greater")$p.value})) 
>           print (paste("successfuly calculated the detection call for
> gene:",g)) 
> } 
> dimnames(p)[[1]]<-geneNames(AffyBatch) 
> a<-cut(p,br=c(0,0.04,0.06,1),include.lowest=TRUE)
> levels(a)<-c("P","M","A")
>  
> d<-matrix(a,nrow=dim(p)[1],ncol=dim(p)[2],dimnames=dimnames(p)) return
> (d) 
> } 
> To use it, write: 
> dc<-DetectionCall(your_AffyBatch) 
> to save it: 
> write.table(dc,file="flags.txt",sep="\t",quote=FALSE,col.names=NA) 
> Ron
> 
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> 
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