Ran into this when a particular file started crashing after performing all the comparisons. It's coming from this line where it checks whether the first abundance value is log2 transformed--if that value happens to be NA (which is going to happen occasionally) then it crashes with the error:
Error in if (abs(log2(temp[1, "INTENSITY"]) - temp[1, "ABUNDANCE"]) < :
missing value where TRUE/FALSE needed
Calls: groupComparison
There are a couple reasonable solutions--just look for the first non-NA value here (it looks like it should be doing that anyway. I have no idea why it doesn't work!), or (probably better) keep track of the log transformation explicitly, rather than using this test to guess what it was.
Ran into this when a particular file started crashing after performing all the comparisons. It's coming from this line where it checks whether the first abundance value is log2 transformed--if that value happens to be NA (which is going to happen occasionally) then it crashes with the error:
There are a couple reasonable solutions--just look for the first non-NA value here (it looks like it should be doing that anyway. I have no idea why it doesn't work!), or (probably better) keep track of the log transformation explicitly, rather than using this test to guess what it was.