[BioC] reg Golub Data set

Dibakar Ray dibakar at hub.nic.in
Tue Sep 2 18:20:11 MEST 2003


Recently I have started working with R and bioconductor package.
I was going through the documentation and tutorial availbale at
bioconductor site. In one of the tutorial the following commands are shown
-
LS<-exprs(golubTrain)
cl<-golubTrain$ALL.AML
TS<-exprs(golubTest)
clts<-golubTest$ALL.AML
##mmfilt is in the library
LS[LS<100]<-100
TS[TS<100]<-100
LS[LS>16000]<-16000
TS[TS>16000]<-16000
mmfilt <- function(r=5, d=500, na.rm=TRUE) {
function(x) {
minval <- min(x, na.rm=na.rm)
maxval <- max(x, na.rm=na.rm)
(maxval/minval > 5) && (maxval-minval > 500)
}
}
mmfun <- mmfilt()
ffun <- filterfun(mmfun)
good <- genefilter(cbind(LS, TS), ffun )
sum(good) ##I get 3571
LSsub <- log10(LS[good,])
TSsub <- log10(TS[good,])
LTsub <- cbind(LSsub, TSsub)
=============
My question is realted to the object good. If I use typeof(good), it shows
logical. So what I understand is good is a logical vector.

But when I type good at the R prompt, it gives me a list of gene name
along  with TRUE FALSE value.
My understanding of logical vector is that it contains elements which are
TRUE or FALSE. So my question is how gene names are accomodated into good.
Thanks
Dibakar Ray



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