MATLAB: Am I getting a warning in “mafdr” when using the list of p-values

Question

I am getting the warning below when trying to calculate FDR for some p-values on a list. Even if I try with a smaller subset of the p-values on my list I get this warning. Could some one please explain why the mafdr function is complaining?

>> pvalues = [0.8708
  0.0709
  0.3546
  0.4540
  0.1767
  0.0333
  0.9174
  0.6118
  0.2853
  0.8558
  0.8419
  0.9736
  0.5124
  0.4884
  0.5656
  0.9730]
>> [fdr qValues] = mafdr(pvalues);
Warning: The estimated PI0 is greater than 1. Please check the p-values are valid
or try a different lambda method
PI0 is set to 1. 
> In mafdr>bootstrapchooser at 316
In mafdr>storeyFDR at 220
In mafdr at 190
>> qValues
qValues =
    0.9736
    0.5668
    0.9736
    0.9736
    0.9426
    0.5333
    0.9736
    0.9736
    0.9736
    0.9736
    0.9736
    0.9736
    0.9736
    0.9736
    0.9736
    0.9736

PS I am new to this kind of analysis and MATLAB.

Answer 1

Hi, that is apparently a bug in the bootstrapchooser helper function. Do you have access to the R2012b prerelease version of MATLAB?

That behavior is fixed in the R2012b prerelease version.