[BioC] EdgeR :column sums of counts or library size?

[Mark Robinson]

Hi Anna,

Short answer is yes, it could/would change the results.  In my experience, these different choices are typically close to each other (or, at least proportional).  It is safest to use a standard analysis (column sums of count table, which you may want to call calcNormFactors on).  As usual, it is always best to LOOK at your data (e.g. plotSmear, in this case) to get a sense of whether these factors have an effect.

Best, Mark


On 08.11.2012, at 00:58, anna [guest] wrote:

> 
> Dear all,
> I was wondering wether it would change the results if we provide the initial library size, the mapped reads number or just the sum of counts to perform an RNAseq analysis,
> thanks in advance,
> anna
> 
> -- output of sessionInfo(): 
> 
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
> 
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
> [5] LC_TIME=French_France.1252    
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] edgeR_3.0.0  limma_3.14.1
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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Prof. Dr. Mark Robinson
Bioinformatics
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