User: Chris Bolen

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Chris Bolen20
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Posts by Chris Bolen

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Comment: C: plot QuSAGE problem
... It's not stored directly, but the indices of the genes are stored in the "pathways" slot of the results. You could use these indices to find out which rows are being used, or you could just use R's "intersect" function on each of your pathways, as follows: sapply(MSIG.geneSets, intersect, rownames( ...
written 6.0 years ago by Chris Bolen20
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Answer: A: plot QuSAGE problem
... Hi Natalia, Sorry about that. Looks like you found a bug in the plotCIs function. The code will have to be fixed, but there are two workarounds that you can use in the mean time. First is to only try to plot non-NA pathways by specifying the path.index parameter, as follows: non.na = which(!is.na ...
written 6.0 years ago by Chris Bolen20

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