Dear Bioconductor members
I am asked to analyze my lab's HTA2.0 data once again, but this time to find information on specific transcript variants.
Do you know if it is possible to annotate an Eset obtained via : data.rma = oligo::rma(data, target="probeset")? For what I understand, this apply RMA to the probeset, without summarizing in transcriptclusters. And can we perform DE analysis on transcripts ?
For instance, how do I know which probes will be of interest for this kind of transcript : https://www.ncbi.nlm.nih.gov/nuccore/XM_011529084.2
I read in an another thread (Use junction probesets (JUC) to detect alternative splicing on Affymetrix human HTA 2.0 arrays? that practically no one was interested in transcript analysis from microarray data, explaining the lack of tools to perform this task. Is it really so ? I find this quite surprising.
Thank you for your help,