Hi Henrik, Thanks for your answer. > 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 preemptively finished. If so, not all units have > been fitted. Rerun with ram=1 to see if you get a different result; > the units already fitted will be skipped.
The memory was not an issue, I did not get any errors doing copy and paste of the code, and results remained the same after using ram=1. I used 500 since I have a 32GB machine. > I'm also not sure if > > 431210/(1190297*107) >  0.003385710 > is an exceptionally large fraction. Agree that this is not a large fraction, I just want to be sure that this does not happen to the most interesting exons :) >Note also that 431210/107 is > exactly 4030; it could be that it is the exact same 4030 units that > are NA in all samples. Yes, maybe I should mention that the NaN values occur for all samples. The group value is 1 for all these 4030 probes with NaN values. Also, the Inf values occur for all samples for 8 probes (various units and groups). unit group cell 001_R887 002_R779 003_R649 144265 3731 237 144265 Inf Inf Inf 179089 4631 149 179089 Inf Inf Inf 180652 4652 234 180652 Inf Inf Inf 193136 5020 183 193136 Inf Inf Inf 204140 5335 145 204140 Inf Inf Inf 269865 7329 135 269865 Inf Inf Inf 306336 8509 364 306336 Inf Inf Inf 513819 16550 132 513819 Inf Inf Inf Regards, Adi -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to firstname.lastname@example.org To unsubscribe and other options, go to http://www.aroma-project.org/forum/