[R] "CV" for log normal data

[Bert Gunter]

Inline below.

On Tue, Feb 21, 2012 at 2:07 PM, Peter Langfelder
<peter.langfelder at gmail.com> wrote:
> 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.

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
>
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

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