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.

Hi Marina. A couple of things would help me understand your problem: -- can you give the output of your sessionInfo() ? For one thing, it looks like you are using an older version of edgeR, so it would be worth trying the latest version. I remember a fix we put in awhile back that accounted for lower-depth datasets that have a lot of ties in the log-ratios. -- what does colSums(counts) and colSums(counts==0) give? > 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 don't understand exactly what this means. Certainly, if you take out columns V4 and V12, there shouldn't be any problem. Alternatively, send me a data matrix off-line and I can take a look. Cheers, Mark On 2011-01-29, at 12:01 AM, Marina Naval Sanchez wrote: > 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 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: mrobinson at wehi.edu.au e: m.robinson at garvan.org.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}