OddsRatio or logOddsRatio ?

[Goutham]

Hi,

I have a question. fisher.test returns the odds ratio ( estimate ). I could not find in the code that the odds ratio is been converted to logOddsRatio. Does the runLOLA outputs odds ratio or logOddsRatio ?

[Nathan Sheffield]

The original version mislabeled the column logOddsRatio. It should have been labled oddsRatio.

This was corrected in commit 1347cca
See this line:

LOLA/R/calcLocEnrichment.R

Line 180 in 0f722fb

 orderedCols = c("userSet", "dbSet", "collection", "pValueLog", "oddsRatio", 

The dev version on bioc is updated so it should be fixed in the next bioc release.

[Nathan Sheffield]

This is now corrected in the released version of LOLA.