Hi, I need to state the reproducibility between sequence lanes for RNA- Seq. I don't think that I can print out a normalized set of count data using TMM but Just the normalization scale factors? How can I print out the 75th percentile scaled Values? If I calculate this 75%-ile counts and then calculate the SD? Would it be best to us the common dispersion values? Lana Schaffer Biostatistics, Informatics DNA Array Core Facility 858-784-2263 [[alternative HTML version deleted]]

Hi Lana, On May 12, 2011, at 2:38 AM, Lana Schaffer wrote: > Hi, > I need to state the reproducibility between sequence lanes for RNA- Seq. > I don't think that I can print out a normalized set of count data using TMM but > Just the normalization scale factors? Well, you can do it manually, something like: normvals <- t( t(counts) / (lib.size*norm.factor) ) * 1e6 ... (1e6 makes it reads per million) > How can I print out the 75th percentile scaled > Values? Similarly: p75 <- apply(counts,2,quantile,p=.75) normvals <- t( t(counts) / p75 ) > If I calculate this 75%-ile counts and then calculate the SD? > Would it be best to us the common dispersion values? Yes, common dispersion is a good reflection of variation between samples/lanes. For tech reps that I've seen, common dispersion is low (e.g. less than 0.01). You may even consider a (Spearman rank) correlation coefficient? Hope that helps. Mark > > Lana Schaffer > Biostatistics, Informatics > DNA Array Core Facility > 858-784-2263 > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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}}