This issue is now resolved.
https://support.bioconductor.org/p/125255/
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel
You’re probably aware of this already, but posting here in case others run into
the BiocCheck and other URL-dependent errors that I ran into this morning.
- Alex
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To your point, a bug is something that happens that wasn't intended by the
develope
Hi Michael,
tx_by_gene <- transcriptsBy(txdb, by='gene') returns a named list (or
more precisely, a named GRangesList object) where the names are the gene
ids. The show() method for these objects actually gives a clue that the
list carries names:
> tx_by_gene
GRangesList object of length 2446
Apologies for a previous email that seems content free.
I've run into a cosmic mis-match between biomaRt and TxDb which is either a bug
or a bug waiting to happen. In brief, biomaRt reports entrezgene_id as a
numeric, but TxDb wants it as a character. What's deadly in this is that TxDb
does
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