Hi,

I am not quite clear about the normalization in edgeR. I am not seeing any change in the actual read counts.

They are same numbers except filtered for >10 reads, library size is reduced and norm.factor is 1.

Could you please comments on this?

Codes:

x<-read.delim("counts.txt",header=T,sep="\t")

y<-DGEList(counts=x[,2:151])
y <- calcNormFactors(y)
str(y)
keep<-rowSums(cpm(y)>10)>=3  
y<-y[keep,,keep.lib.sizes=FALSE]
str(y)
head(y$counts)
y$counts
# recaclulate the library size
y<-DGEList(counts=y)
y$samples  

Well, you reset all the normalization factors back to 1 when you ran DGEList() again at the end. Why did you do that? The library sizes had been recalculated already.

Have you read the section on normalization in the edgeR User's Guide? Amongst other things, that tells you why the read counts themselves are never changed.

Minor points:

I think it is usually better to run calcNormFactors() after filtering rather than before.

There is no need for str(y). Just type show(y) or just y by itself. It's far more informative.