i am currently working with TCGA dataset from UCSC xena browser. I have completed the differential gene expression analysis using Deseq2 from genepattern for one cancer dataset. I have some doubts regarding the result and want to know how to proceed further for analyzing across different cancer samples. I am very new to TCGA and currently doing the analysis based on
Following are my doubts regarding the analysis
1. HT seq count file downloaded from xena has transcript id's, i want gene id's for my analysis. How should i do this?
2. For generating a heatmap for DEG's of different cancer dataset should i use the log2 expression values from DEseq2?