[aroma.affymetrix] non finite values in FIRMA results

2010-08-02 Thread Adi Tarca
Hi all, I have a batch of 107 mice exon arrays for which I computed FIRMA scores and I got many NaN, Inf and 0 values which disable further analysis based on log FIRMA values for some probesets. I was wondering if this is a known issue or I am the only one to get these results. Here is the code

Re: [aroma.affymetrix] non finite values in FIRMA results

2010-08-02 Thread Henrik Bengtsson
Hi, I'll leave the details to FIRMA experts, but you are using really large values of argument 'ram'. It might be that you ran out of memory (the you got an error message). If you used cut'n'paste, instead of source(), to do the analysis, it might be that one of the fit() methods was