I have a difficult experiment and I need some advice on how to proceed.
I have a data set of ~400 human rnaseq samples from different risk groups and as subgroup various abnormalities. I'm interested in finding out whether there is a significant difference in the expression of two specific transcripts of the same gene between two conditions. What I mean is, I would like to know if the difference of expression of TX1 between condition1 and condition2 is significantly higher/lower than the expression differences of TX2 between the same two conditions.
I don't know how to run this analysis!
What I have tried so far was as follow - I have done
DEXSeq, but all they give me is the significance of a specific gene between two conditions. Even if I run it on transcript level, I can only find out if TX1 is significantly expressed between condition1 and condition2.
I have already asked a few questions (e.g. here, or here) about this experiment previously, but they didn't realy helped me much. I think my problematic was not understandable, so i hope i have made it clearer here.
for completeness, I have also run
Kallisto (with bootstrapping) &
Salmon on the complete data set. I have now a list of the counts from
Kallisto on transcript level and on gene level (imported by
tximport) and the TPM values calculated by Kallisto and by Salmon. But I still can only compare one transcript between two conditions.
I can't seem to find a way to analyse the data in the way I need it and get the results for a comparison of two transcripts over two conditions.
I would your advice on how to analyse the data. Is there a statistical robust way to analyse this kind of data?