"Error in if (relI < 0) { : missing value where TRUE/FALSE needed"

[ethanbass]

I am getting an error in the runGC function, when it gets to the following part:

ann.df <- getAnnotationMat(exp.msp = allSamples.msp, pspectra = PseudoSpectra,

•                        allMatches = allSam.matches)
  

It throws an error:
"Error in if (relI < 0) { : missing value where TRUE/FALSE needed"

I was trying to troubleshoot it on my own, by going through the function line by line, but I can't find the 'relInt' function that seems to be causing the problem.

[persaj]

@ethanbass was this issue fixed?

I'm having the same problem

Maybe @rwehrens can help?

[ethanbass]

@persaj, I know I got it to work, but now I can't remember what the problem actually ended up being. Maybe if you post some the files that you are having trouble importing, I could look at it.

[persaj]

Thanks @ethanbass, I don't know how to extract all the files from R, does it help if I share the .Rproj file?

[ethanbass]

Sure, we can try that. I'm not sure you will be able to host it on github if it's more than 100 MB though?

[persaj]

@ethanbass the settings that we used gave NA's, but we've worked out a fix.
We worked around the NA by adding the code if (**is.na(relI) |** relI < 0) in the last part.
Below the code that can be used:
Fix_getannotationsmat.txt