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Bioconductor / AnnotationHub

Client for the Bioconductor AnnotationHub web resource
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AnnotationHub and GO Terms #51

Closed famfigueiredo closed 4 months ago

famfigueiredo commented 4 months ago

As a follow up of this question, while I was able to replicate the analysis by using the same version of R and Bioconductor used at the time, I would like to understand the source of the discrepancies between using the AH107424 annotation file in 2022 and AH114250 in 2023.

The issue is that I do not get the same GO Terms through enrichGO with both annotation files. Since the AH114250 annotation file is quite recent, is it a question of the annotation with GO Terms 'catching up'? Plotted in 2022 using older Atlantic salmon annotation file. Downregulated (A) vs Upregulated (B). ora_downreg_vs_upreg_4WPC

Plotted in 2024 using more recent Atlantic salmon annotation file dnavaccine_vs_conu_4wpc_resized

lshep commented 4 months ago

These types of questions are better asked on the support site and only report bugs or feature requests in issues. We generate the objects based on data at ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ . You can look at the README to find out how these files are updated.