Inline below. On Tue, Feb 21, 2012 at 2:07 PM, Peter Langfelder <peter.langfel...@gmail.com> wrote: > 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.
Good advice. But perhaps ?mad or some other perhaps robust plain old measure of spread? -- Bert > > 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm ______________________________________________ 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.
