I am a beginner in RNA-seq analysis. Recently, I was trying to analyze the differential expression of a particular isoform in cancer vs normal sample from TCGA exon specific data. I found that all the exons of a particular isoform has different reads/RPKM value. What I was thinking-if a full length isoform is expressed in a particular cell, all the exons of this isoforms should be expressed at the same level. Please correct me if this is not true.
Another thing is that-if I want to compare the expression of a particular isoform in cancer vs normal cell, do I have to compare the total reads/RPKM from all the exons in each condition (cancer vs normal)?