I am looking for a method to compare the significance of the expression difference of two different transcripts within a specific condition.
with that said, i will try to explain a bit more. We have a RNA-Seq experiment with three conditions. We are comparing each pair of conditions to find significant differentially regulated genes on gene (deseq2,cuffdiff) and transcript level (kallisto,cuffdiff,dexseq).
For some of the transcripts (isoforms of the same gene) we would like not only to know whether or not they are significant DE between the two conditions, but also if transcriptA is significantly higher/lower expressed than transcriptB.
About the data - we have 10 replicates for each of the three conditions.
For the first question I have done done the calculations with the mentioned tools. I am struggling to find a way to calculate the second problem. Is there a method to calculate such significances?
thanks for the help,