Hi Adi. First, you seem to be doing the FIRMA analysis on probeset-level data (i.e. roughly 4 probes per exon), using the fullR1,A20080718,MR. FIRMA is really a method that uses all of the probe-level data for an entire *gene* and then summarizes residuals to score differential splicing at the probeset level. You'll therefore want to use a CDF file that is oriented this way (perhaps MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf or MoEx-1_0-st-v1,U-Ensembl50,G-Affy,EP.cdf?)
I think the NaNs you get are just from the fact that some exons only have a single probe (and, as you say, group=1 below!). Cheers, Mark On 2010-08-02, at 7:49 PM, Adi Tarca wrote: > 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) >> [1] 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 aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- 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 aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
