[BioC] TMM factors

[Mark Robinson]

Hi Sooby,

Some comments below.

On 20.04.2012, at 04:32, Sooby wrote:

> Hi all,
> I met a question when I analysed mRNA data. I use TMM provided in edgeR to normalizition my data. After I got the factors, How Do I treat my raw counts?? In my oppion, (raw.counts)*10^7/(librarysize*factors),Is It right?

So, this is correct, for a reads per 10M conversion.  I'm not sure what you mean by "treat my raw counts".  If you are doing differential expression with edgeR (or DESeq, etc.), we strongly suggest to use the raw counts, without "treating" them.


> And another question is which librarysize do I need? The unique total reads or the reads mapped to each gene???

Usually, total number of mapped reads.

Best,
Mark

> I need your help~~~
> Best 
> 
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