Hi everyone, I am working on Affymetrix Human Exon Arrays and in order to perform an analysis on every possible exon on the array, I would like to use the "fullR3" CDF (see http://www.aroma-project.org/chipTypes/HuEx-1_0-st-v2/transcriptClustersCDFs ). Now, I just came across a thread stating that it makes more sense to use core probes instead in order to derive true gene expression levels (see http://email@example.com/msg01571.html). In my opinion this limits the overall discovery rate, since a number of genes is not included in the core annotation and thereby missed completely. Thus, I was wondering whether it is possible to estimate the gene expression level via core or extended probes and then calculate the deviation/FIRMA scores for full probes as well.
Best regards -- -- 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 firstname.lastname@example.org To unsubscribe and other options, go to http://www.aroma-project.org/forum/