[BioC] edgeR calcNormFactors NaN

[Marina Naval Sanchez]

Hi all,


when doing calcNormFactors using edgeR I obtain some NaN values.

f=calcNormFactors(counts)
       V2        V3        V4        V5        V6        V7        V8        V9 
1.0000000 0.9987462       NaN 0.7550607 0.6139919 0.8603117 0.8594895 0.7910109 
      V10       V11       V12       V13       V14       V15       V16       V17 
0.7967414 0.7837294       NaN 0.8136299 0.8136299 0.8136299 0.8136299 0.8679718 
      V18       V19       V20       V21 
0.8575024 0.8575024 0.8575024 0.8575024 




I checked if I had some errors in my columns but I could not find andy NA in my data. On the other hand when I take a subset of the columns including the ones giving me f NaN v4 and v12 

I do not obtain NaN anymore.  I would like to know what is producing this effect. I tried to look at the calcNormFactors but I do not know what calcFactorWeightted does.

function (dataMatrix, refColumn = 1, logratioTrim = 0.3, sumTrim = 0.05, 
    doWeighting = TRUE, Acutoff = -1e+10) 
{
    if (!is.matrix(dataMatrix)) 
        stop("'dataMatrix' needs to be a matrix")
    if (refColumn > ncol(dataMatrix)) 
        stop("Invalid 'refColumn' argument")
    apply(dataMatrix, 2, .calcFactorWeighted, ref = dataMatrix[, 
        refColumn], logratioTrim = logratioTrim, sumTrim = sumTrim, 
        doWeighting = doWeighting, Acutoff = Acutoff)
}


Thank you very much.