Naive question:
For calcNormFactors(), while using method="TMM", for normalization, can
multiple independent biological replicates be used to normalize against?
Help on calcNormFactors in edgeR seems to indicate using only one reference
library / column (copied and pasted below).
Could someone please clarify?
Thanks,
AksR

Usage:

     calcNormFactors(object, method=c("TMM","RLE","upperquartile"),
refColumn = NULL, logratioTrim = .3, sumTrim = 0.05, doWeighting=TRUE,
Acutoff=-1e10, p=0.75)

Arguments:

  object: either a ‘matrix’ of raw (read) counts or a ‘DGEList’ object

  method: method to use to calculate the scale factors

refColumn: column to use as reference, only used when ‘method="TMM"’

logratioTrim: amount of trim to use on log-ratios ("M" values), only
          used when ‘method="TMM"’

 sumTrim: amount of trim to use on the combined absolute levels ("A"
          values), only used when ‘method="TMM"’

doWeighting: logical, whether to compute (asymptotic binomial
          precision) weights, only used when ‘method="TMM"’

 Acutoff: cutoff on "A" values to use before trimming, only used when
          ‘method="TMM"’

       p: percentile (between 0 and 1) used to compute scale factors
          from, only used when ‘method="upperquartile"’

Details:

     ‘method="TMM"’ is the weighted trimmed mean of M-values (to the
     reference) proposed by Robinson and Oshlack (2010), where the
     weights are from the delta method on Binomial data.  If
     ‘refColumn’ is unspecified, the library whose upper quartile is
     closest to the mean upper quartile is used.


-- 
Anand K.S. Rao
PhD candidate
Plant Biology Graduate Group
President
Indian Graduate Student Association @ UCDavis
University of California at Davis
Davis, CA - 95616 USA
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