[BioC] Go terms attributes not available on Biomart ensembl
chawla
chawla at bio.ntnu.no
Sun May 15 23:53:43 CEST 2011
Hi
I have used BiomaRt to retrieve GO terms for affymetrix probe Ids using
mart ensembl.
But suddenly all the GO terms attributes have vanished from the list of
attributes.
I used the sample code to test.
> affyids = c("202763_at", "209310_s_at", "207500_at")
> getBM(attributes = c("affy_hg_u133_plus_2",
"go_biological_process_id", "chromosome_name", "start_position",
+ "end_position", "band"), filters = "affy_hg_u133_plus_2", values =
affyids, mart = ensembl)
Error in getBM(attributes = c("affy_hg_u133_plus_2",
"go_biological_process_id", :
Invalid attribute(s): go_biological_process_id
Please use the function 'listAttributes' to get valid attribute names
I am thus unable to reproduce previous results.
Have no idea how this could happen, If anyone can help it will be great.
Thanks
Konika
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