Hi Sabrina. Sorry for the slow reply.
Basically, there isn't a lot of precedent for this, but I would suggest using all 16 arrays to define the FIRMA scores. Then use limma on those to look for your differences of interest. My reasoning is that this will allow the data from more arrays to be used for the estimation of probe effects. Hope that helps. Mark On 2011-01-04, at 7:29 PM, sabrina wrote: > Hello, all: > I have 16 exon arrays from 4 groups, A1, A2 and B1, B2. As are > genetically identical but with different treatment,Bs are genetically > identical (but different from As) with different treatment 1 and 2. I > am interested in finding alternative splicing events that was affected > by treatment on A and B and also by genetics (under same treatement). > Therefore, the comparison I am interested are A1 vs. A2, B1vsB2, A1 vs > B1 (only treatment 1) . My question is, when I do RMA and calculate > the FIRMA score, do I use all 16 array I have to get Firma scores, > then use limma as suggested before to apply to design matrix and > contrast matrix? Or should I for each comparison , do RMA and FIRMA > score for exon arrays only involved in that comparison? Thanks for > your input! > > Sabrina > > -- > 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: mrobin...@wehi.edu.au e: m.robin...@garvan.org.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/
