Question: TMM and calcNormFactors: Normalization in baySeq to match, edgeR and DESeq (Smith, Hilary A)
gravatar for Thomas J Hardcastle
7.8 years ago by
United Kingdom
Thomas J Hardcastle180 wrote:
On 18/11/11 11:00, bioconductor-request at 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
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