Leo pointed me in the direction of your question. I'm not positive where/how Firebrowse filtered their data (as I'm less familiar with that resource and didn't look into it) to reach 185 samples; however, I think I may have found the answer to your question. It looks as though the 185 samples are tumor type samples, while the other 13 are 'normal types' (see code below). TCGA barcode explanations can be further explored here.
## download metadata for recount TCGA data
recount::all_metadata('TCGA') -> md
## just look at the Esophageal samples
md_sub = subset(md,md$xml_primary_pathology_tumor_tissue_site=="Esophagus")
## take a look at sample type information
# Tumor types range from 01 - 09, normal types from 10 - 19 and control samples from 20 - 29
01 06 11
184 1 13
Let me (er...us) know if anything is unclear or you have further questions!
modified 21 months ago
21 months ago by
sellis18 • 20