Hi, I downloaded HARMONIZED miRNA data from TCGA. The dataframe have two columns 1)reads_per_million_miRNA_mapped_TCGA-HC-7211-01A-11R-2117-13 and 2) raw_count_miRNAs.
1. Should I use reads_per_million or raw_counts to compare DE miRNAs ?
2. I believe the "reads_per_million_miRNA" is already converted to CPM and normalized. IF yes, can I use the values straight away ?
3. If I use "reads_per_million_miRNA" straight away, shall I just remove miRNAs with "0" values ?
4. Same questions when I use "raw_counts_miRNAs"