So I have RNAseq read count data from two different sources.
First one is from TCGA level-3 data , which has 'raw_counts' coulmn for each gene.
Second one is from a GEO dataset, where the submitter has provided "scaled_counts" for each gene. I guess its calculated from estimateSizeFactors() from DESeq.
Now, how do I compare these count tables, one is normalized/scaled and the other one is raw ?
Do I just scale the unscaled tcga data and compare with the other one or do I have to combine both the tables and scale it before proceeding?