I am studying a group of cancer patients from which I have INDELs (from DNA fastq) and expression data (RNAseq), both from a tumoral and a normal sample for each one of them.
As I know some genes affected by potential pathogenic insertions or deletions, I would like to assess, for each patient, an effect of the alteration in its expression. As this analysis is performed individually for each patient, as these mutations are unique, I am not sure how to perform it statistically. I would like to compare the expression levels between tumour and normal sample for each individual patient. As the comparisson is between two samples, I cannot perform an usual differencial expression analysis.
How can I achieve this?