[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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