[R] "CV" for log normal data
peter.langfelder at gmail.com
Tue Feb 21 23:07:16 CET 2012
On Tue, Feb 21, 2012 at 1:44 PM, array chip <arrayprofile at 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.
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