[BioC] Error when running limma on low variance data

Chao-Jen Wong cwon2 at fhcrc.org
Thu Sep 10 21:57:23 CEST 2009


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



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