Dear bioC community,
I have spent more than a whole day searching for tutorials/manuals to analyse mouse transcriptome arrays 1.0. I want to perform a DE analysis gene-wise but considering only exons, and there's apparently no information in the web. And what's the difference between mta10stprobeset and mta10sttranscriptioncluster? Does one consider the probes and the other the probesets? In that case, how can I distinguish probes mapping to exons, junctions and others? Is there any function for that? When I use mta10sttrancriptioncluster and limma to analyse DE genes, about 50% are DE, which makes no sense. Could any kind soul help me please?
Thanks in advance