[BioC] how to get normalized matrix

[Mark Robinson]

Hi Eyal,

You might read the posting guide:
http://www.bioconductor.org/help/mailing-list/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:

?cpm

Best, Mark



On 04.10.2012, at 16:21, eyal avisar wrote:

> hello,
>  
> 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)
>> library(limma)
>> raw.data <- read.delim("myFile.txt")
>> names(raw.data)
>  d <- raw.data[, 2:64]
>  rownames(d) <- raw.data[, 1]
>  
> i did not group, irrelevant for me
>  d <- DGEList(counts = d)
>  dim(d)
>  
> result was [1] number... 3
>  > cpm.d <- cpm(d)
>> d <- d[ rowSums(cpm.d > 1) >=3, ]
>> d <- calcNormFactors(d)
>  
> thx,
>  
> Eyal_______________________________________________
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