Hypothesis testing for isoform level TCGA RNA-seq expression data
I am working with isoform-level RNA-seq data from TCGA. After calculating isoform fraction (expression level of a particular isoform divided by the total expression of all the isoforms belonging to a gene) for all isoforms in cancer and tumor samples I wanted to check if the expression of a particular isoform is different between normal and cancer patient samples. To achieve this, I made a boxplot using this data but without any p-value because I did not perform any hypothesis test on this data. What kind of test can be performed on this kind of data?
PS: I am new to bioinformatics analysis, so any links to other online forums pertaining to the question would help.
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This comes down to differential transcript analysis. Use established tools such as https://bioconductor.org/packages/release/bioc/html/fishpond.html,
kallisto/sleuthorDEXSeqand then check if your isoform is among the DETs.