Hi all. I would like to filter my Affymetrix data using the mas5calls function in Affy package. For example, I would like to only look at genes which are called present at least twice in 20 chips, and remove genes which are always absent. Not sure how to go about this. Regards Anthony -- ______________________________________________ Anthony Bosco - Cell Biology Research Assistant Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au

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(AffyBatch,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 [[alternative HTML version deleted]]

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@wisemail.weizmann.ac.il] > Sent: 08 December 2003 08:48 > To: bioconductor@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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo> /bioconductor > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}