Access edgeR test statistic
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Entering edit mode
2.0 years ago
rrcutler ▴ 120

I'd like to know an easy way to access test statistics calculated after using the exactTest() function in edgeR. I'd like to use these with fdrtool to attempt to estimate corrected FDR values due to a skewed p-value distribution. Currently, in the object produced by this function, I can only access:

> colnames(res\$table)
[1] "logFC"  "logCPM" "PValue" "FDR"


Thanks, R

edgeR • 547 views
1
Entering edit mode
2.0 years ago
Gordon Smyth ★ 2.5k

exactTest conducts the exact negative binomial test directly from the data, so the p-values are not computed via a test statistic.

topTags already computes FDR bounds using the Benjamini-Hochberg method. In this context I would recommend Benjamini-Hochberg over fdrtool anyway because it is more conservative and makes fewer assumptions.