[BioC] Error when running limma on low variance data

[Chao-Jen Wong]

Hi, Qianqian,

As Gordan mentioned,  you can try to  filter out probes that are lack of
variation by using 'nsFilter' or 'varFilter' functions in the genefilter
package. Hope this would help.

Chao-Jen

qq bioconductor wrote:
> Dear list member,
>
>   I got an error message when running limma on my array dataset, which
> contains a total of four Affy arrays from two different conditions.
>
> Error in if (evar > 0) { : missing value where TRUE/FALSE needed
> In addition: Warning message:
> In fitFDist(var, df1 = df) :
>   More than half of residual variances are exactly zero: eBayes unreliable
>
> I found the variances of most probesets in my dataset is 0. Therefore
> median(fit$sigma^2) is 0.
> The error is because in my case the "evar" variable in function fitFDist is
> NaN, which is because some elements in the "e" variable are equal to -Inf
> and "emean" is -Inf.
> (    emean <- mean(e)
>     evar <- mean(n/(n - 1) * (e - emean)^2 - trigamma(df1/2))
> )
>
>
> Does anyone know how I can fix the error? Thank you!
>
> Sincerely,
> Qianqian
>
> 	[[alternative HTML version deleted]]
>
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-- 
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M2-B876
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org