Hi,
I looked at the results, fg,
> names(fg)
[1] "mufScores" "firmaGeneScores" "nProbe"
[4] "nullDistributions" "nProbeNull" "plmObject"
[7] "cls"
There is no Pvalue (or Qvalue), but the paper says:
"To alleviate this, we repeatedly sample J probes from
the empirical distribution of all standardized residuals
and calculated the MUF score, giving a null distribution of
MUF scores for J probes. A false discovery rate can be calculated
for the discoveries above a given quantile of the
null distributions."
How can I get the Qvalue from false discovery rate ?
Thanks,
Qicheng
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