Hi Sabrina. Tricky question.
Do you have biological replicates of some samples and technical replicates of others? Or, just technical replicates of everything? I suspect it would be difficult to justify adding a bunch of extra (adhoc) steps into the FIRMA pipeline. I don't have a full understanding of your experiment, but what about just dealing with it when you operate on the FIRMA scores? When you say "average on plm", I assume this means an average of the chip effects for those two samples? You could fit a PLM that estimates a single chip effect for those two samples and use that for calculating FIRMA scores. Hope that helps. Cheers, Mark On 20/01/2009, at 9:09 AM, sabrina wrote: > > Hi, all: > I am working on Affy Mouse Exon Array . Because of the experiment > design and quality of the hybridization, we have two arrays hybridized > from one mouse (same biological sample). I assume that I should treat > these two arrays as tehcnical duplicates. If that is the case, I could > do background correction, normalization and summary separately for > these two arrays,(RMA, and ExonRmaPlm), then before I use FIRMA to > get firma scores, can I just do average on plm of these two arrays? > But then what do I feed in FIRMAModel? ( The default one is just plm > results directly from ExonRmaPlm) .Or any suggestions about how to > deal with this situation? My goal is to find novel splicing events, > but right now I am just using core annotation to try it out. Thanks! > > Sabrina > > ------------------------------ Mark Robinson 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 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
