[BioC] how to get normalized matrix
mark.robinson at imls.uzh.ch
Thu Oct 4 23:12:21 CEST 2012
You might read the posting guide:
I don't really understand your question, but from your subject and your cryptic description, I think you've used the right function - cpm() - to get a normalized matrix. You might also consider using :
cpm.d <- cpm(d, normalized.lib.sizes=TRUE)
More description by typing:
On 04.10.2012, at 16:21, eyal avisar wrote:
> my name is Eyal and i am new to R, cut and paste level.
> i have created a DGEList object - d following case study 3.3.3.
> i ran the calcNormFactors(d).
> the output i need is a normalized table.
> > library(edgeR)
>> raw.data <- read.delim("myFile.txt")
> d <- raw.data[, 2:64]
> rownames(d) <- raw.data[, 1]
> i did not group, irrelevant for me
> d <- DGEList(counts = d)
> result was  number... 3
> > cpm.d <- cpm(d)
>> d <- d[ rowSums(cpm.d > 1) >=3, ]
>> d <- calcNormFactors(d)
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