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hammerlab / multi-omic-urothelial-anti-pdl1

Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis
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question about your data #3

Open zhangyonglzg opened 6 years ago

zhangyonglzg commented 6 years ago

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 commented 6 years ago

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.