Thanks Mark, Using the core cdfs for both human and mouse I still get a few probesets with NaN values but indeed they have 1 probe per probeset only. I was wondering also from what probe values the MAD statistic is computed that is used to scale the residuals and compute the FIRMA scores. The FIRMA paper does not say this clearly. Is it from the exon probes or is it from the transcript probes. I have seen the http://aroma-project.org/node/81 message and I can see there that the scaling factor (variable u.mad) is a constant for the entire dataset (whole samples and whole transcripts and whole exons) therefore I am not sure I understand how this scaling makes the scores comparable between exons and transcripts.
Thanks, Adi On Aug 5, 9:34 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote: > 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 -- 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/
