Hi!
I'm looking through your code @sr320 --> code here: project-pycno-multispecies-2023/code/38-degs-orth-GOenrichment.Rmd
For the background, based on this blurb:
- **Background / universe** = *all* annotated transcripts for that species
(`09/10/11-annot-*/*_transcript_counts_annotation.tab`) that are likewise
(a) assigned an Orthogroup (from `37-orthofinder/Orthogroups.tsv`) and
(b) carry ≥1 GO ID.
It sounds like you did not use one background for all three? Did you use the annotated proteins that had orthogroups assigned for each species?
I thought that we wanted to try with the same background for all three species -- the list of uniprot-accession IDs associated with orthogroups shared across all three species' protein lists
thanks!
Hi!
I'm looking through your code @sr320 --> code here: project-pycno-multispecies-2023/code/38-degs-orth-GOenrichment.Rmd
For the background, based on this blurb:
It sounds like you did not use one background for all three? Did you use the annotated proteins that had orthogroups assigned for each species?
I thought that we wanted to try with the same background for all three species -- the list of uniprot-accession IDs associated with orthogroups shared across all three species' protein lists
thanks!