[BioC] TMM and calcNormFactors: Normalization in baySeq to match, edgeR and DESeq (Smith, Hilary A)

[Thomas J Hardcastle]

On 18/11/11 11:00, bioconductor-request at r-project.org wrote:
>     9. TMM and calcNormFactors: Normalization in baySeq to match
>        edgeR and DESeq (Smith, Hilary A)
>    

Hi Hilary,

The 'edgeR' function 'calcNormFactors' used to contain an option for 
'quantile', but no more; alas! The baySeq 'getLibsizes' function is 
still trying to call this version, and failing. I will put in a fix for 
this now that it has been brought to my attention, but in the meantime 
the following code should work:

d <- DGEList(counts = cD at data, group = cD at replicates)
d <- calcNormFactors(d)
cD at libsizes <- d$samples$norm.factors


Best wishes,

Tom Hardcastle


-- 
Dr. Thomas J. Hardcastle

Department of Plant Sciences
University of Cambridge
Downing Street
Cambridge, CB2 3EA
United Kingdom