Dear all, I fairly new to the field of Exon Arrays and my experiences with Microarrays in general are quite limited, so I have a couple of questions concerning the analysis of Exon Array data.
First of all, I would like to do an RMA (or GCRMA) based on the validated genes of the core probeset (so bg, qn + sum). The way I understood the literature, this normalizes ALL probesets based on the intensity values of the core probeset (which is also what I intend to do). Afterwards, I want to extend my analysis on the full probeset, as I will focus on some genes that are not included in 'core'. I read about this procedure in a paper on APT and R by H. Lockstone and wanted to implement it via aroma. Am I mislead in this case? I tried to realize this by doing a GCRMA on 'core', but the resulting probe intensities are to few (~285k) and the probes I'm looking for are not included. Before that, I did a regular RMA on the full probeset and I got all the probes /the intensities I was looking for, but I realized that normalizing to not validated genes may not be the best idea. It would be a great help if you could set my thoughts straight and if I'm correct tell me how to use aroma to achieve what I want. Note: I assembled my script as described in http://aroma-project.org/node/37 and https://groups.google.com/forum/#!topic/aroma-affymetrix/QD6o-3XiifM/discussion Thank you in advance for your help. With best regards, Rene -- 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/
