On Tue, Feb 21, 2012 at 1:44 PM, array chip <arrayprof...@yahoo.com> wrote: > Hi, I have a microarray dataset from Agilent chips. The data were really log > ratio between test samples and a universal reference RNA. Because of the > nature of log ratios, coefficient of variation (CV) doesn't really apply to > this kind of data due to the fact that mean of log ratio is very close to 0. > What kind of measurements would people use to measure the dispersion so that > I can compare across genes on the chip to find stably expressed genes? > something similar to CV would be easily interpreted? >
You may want to ask this question in the bioconductor list since it isn't really an R question. Do you also have some sort of an expression p-value? If you only have expression itself, you could simply look at variance and hope that non-expressed genes have expression values determined chiefly by noise which varies quite a bit, so they would have a higher variance than genes with stable expression higher than the typical noise. HTH, Peter ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
