problem with biomart---give 0 results

[angel-sakura]

Hi everyone:

I'm trying to convert ensembl-peptide-id to GO-id with biomart. However, when I was using the following command to run it, I got 0 results.

Here are commands I was using:
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
id_list=c("ENSP00000298510","ENSP00000474109")
trans_id=getBM(attributes=c("ensembl_peptide_id","entrezgene","go_id","name_1006","definition_1006","namespace_1003"), filter="ensembl_peptide_id", values="id_list", mart=ensembl)

Could someone tell me what cause the problem please?

Thanks a lot~

[SylvainL]

In my code, I use filters instead of filter, don't know which version you are using....

[angel-sakura]

In my code, I use filters instead of filter, don't know which version you are using....

Thank you very much for your reply.
I'm pretty sure it is not the problem of typo, as it was working with the example data with the same commands.

[SylvainL]

Ah...

did you update your biomaRt package? Then you have to check whether "ensembl_peptide_id" is still the proper filter name... I had this problem once with biomaRt, with "ensembl_gene_id"

[blancha]

Remove the commas around id_list.

Incorrect.
trans_id=getBM(attributes=c("ensembl_peptide_id","entrezgene","go_id","name_1006","definition_1006","namespace_1003"), filter="ensembl_peptide_id", values="id_list", mart=ensembl)

Correct.
trans_id=getBM(attributes=c("ensembl_peptide_id","entrezgene","go_id","name_1006","definition_1006","namespace_1003"), filter="ensembl_peptide_id", values=id_list, mart=ensembl)

[angel-sakura]

Remove the commas around id_list.

Incorrect.
trans_id=getBM(attributes=c("ensembl_peptide_id","entrezgene","go_id","name_1006","definition_1006","namespace_1003"), filter="ensembl_peptide_id", values="id_list", mart=ensembl)

Correct.
trans_id=getBM(attributes=c("ensembl_peptide_id","entrezgene","go_id","name_1006","definition_1006","namespace_1003"), filter="ensembl_peptide_id", values=id_list, mart=ensembl)

Thank you very much!!!
It is working now!!

[angel-sakura]

Ah...

did you update your biomaRt package? Then you have to check whether "ensembl_peptide_id" is still the proper filter name... I had this problem once with biomaRt, with "ensembl_gene_id"

The problem is solved!!
The "value" doesn't need the quotation mark!

[SylvainL]

Can't believe I didn't see it...

So for your future scripts:
"object" means it's not a variable but a value
object (without ") refers to an existing object.

In your case, it was looking to "id_list" as an "ensembl_peptide_id", meaning if you replace "id_list" by "ENSP00000298510" in your first command, it will give you the results for this protein...

Hope I'm clear enough

[angel-sakura]

Yes! I understand it now!! lol

Thank you so much!