Goodmorning,
I am trying to use the ESTIMATE package to get immune and stromal score for a database containing microarray mRNA data (Affymetrix) in a cohort of 64 cases.
I start with 16158 unique genes (I have selected only one probe per gene), and I have both the Entrez ID and the gene symbol.
When I apply the filterCommonGenes from the vignette, I get the following result:
"Merged dataset includes 8866 genes (1546 mismatched)."
The numbers are similar, both with Entrez ID and with gene symbols, but it is not clear to me what the "match" is based on.
I thought it was a mismatch in gene symbols, but it happens when I use Entrez ID as well.
Can anyone help me?