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

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