Dear all,

I have a problem with the PSICQUIC package while mapping gene name synonyms. Here are the command lines :

# data fetching

tbl.big <- PSICQUIC::interactions(psicquic, species="9606",provider=DB, type="direct interaction”)

#mapping

idMapper <- IDMapper("9606")

tbl.big.2 <- addGeneInfo(idMapper,tbl.big)

However, the last step now fails with the message:

Error in getBM(filters = filter, values = uniprots, attributes = columns,  : 

Invalid attribute(s): uniprot_swissprot_accession 

Please use the function 'listAttributes' to get valid attribute names

I cannot figure out what had changed, since this was working well before, and since the example provided in the vignette is also fine...

Thanks for your help

Anaïs

Hi Anaïs,

Biomart changed the name of this attribute to simply "uniprot_swissprot" about the first of the year.  We discovered this -- just as you did! -- and made the fix in PSICQUIC version 1.5.7.

biocLite("PSICQUIC")   ought to solve the problem.

- Paul

Many thanks, I should have thought about updating before complaining!!

Anaïs