Hi, I have a question. The mean value of the Expression & CN for a gene with more than one transcript is obtained using the more expressed transcript value of that gene or the average of all the transcript’s expression values? I’ve searched on the RNAseq procedure documentation, but I could not find this information.
(For example, 3 in the case of BRAF, gene with more the 20 transcripts)
Hi, if you’re referring to the gene level expression files, we use RSEM outputs and combine TPM values per gene (add them across isoforms for the gene). For CNV we directly calculate the copy number from DNAseq data, so there is no isoform counting involved.
