Dear List
I am currently running a microarray analysis on the dataset schizo and would
like to filter out all genes with a low variance. However, when running the
code detailed below, I end up with 12,500 genes in my final set rather than
the 10,000 I was looking for. Can anyone pinpoint where I am going wrong?
***********reading in data**********
schizo<-read.table("octassign_data.txt",header=T, sep="\t")
dim(schizo)
head(schizo)
attach(schizo)
***********creating matrix and calculating variance across probesets********
x<-c(1:20000)
y<-c(2:151)
schizo.matrix<-data.matrix(schizo[,y])
varprobe<-c(var(schizo.matrix[x,]))
hist(varprobe)
**************filter out low variance*************
top10000 <- which(rank(varprobe)>10000)
schizo.sub<-schizo[top10000,]
>dim(schizo.sub)
[1] 12500 151
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