question about your data

[zhangyonglzg]

Is your file,“multi-omic-urothelial-anti-pdl1/analyses/bladder-kallisto-tximport.csv” representative gene expression matrix on each sample ? And is it processed by RNA-seq?

[tavinathanson]

Hey @zhangyonglzg, this is RNA-Seq data processed with Kallisto to get transcript-level abundances per patient (you can see the Kallisto output files at http://doi.org/10.5281/zenodo.546110), and then processed with tximport (in https://github.com/hammerlab/multi-omic-urothelial-anti-pdl1/blob/master/analyses/Ranalyses/bladder-deseq.R) to get gene-level abundances per patient.