Hi,
I get the following error when trying to build a TxDb object from Biomart. In the forum it is suggseted to build the a TxDb from a gft file. Anyway, I think that command should work and would apreachiate if you might help me to understand what is going wrong.
Thank you very much!!!
> Ensembl_annoTxDb=makeTxDbFromBiomart(biomart="ensembl",
+ dataset="mmusculus_gene_ensembl",
+ transcript_ids=NULL,
+ circ_seqs=DEFAULT_CIRC_SEQS,
+ filter=NULL,
+ id_prefix="ensembl_",
+ host="www.ensembl.org",
+ port=80,
+ taxonomyId=NA,
+ miRBaseBuild=NA)
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Error in function (type, msg, asError = TRUE) :
Recv failure: Connection was reset
This seems to work for me.
Can you include the output of the command
sessionInfo()
, so we can see what versions of packages you're using. Here's mine for comparison.