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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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GEDI package #77

Open Maryan12m opened 1 year ago

Maryan12m commented 1 year ago

Hello

When using GEDI, when ID mapping is done using the biomaRt R package, the following error occurs: Connecting to BioMart... "Error in GEDI(datasets, attributes = attr, BioMart = TRUE, species = "btaurus", : Could not connect to BioMart. Check your internet connection" While the Internet is connected and the biomaRt package is called. How can I solve this problem? I will be grateful for advice.

grimbough commented 1 year ago

Hi @Maryan12m ,

It's hard to know what the issue is without some more information, and I don't know the GEDI package to suggest any advice for that specifically.

I'd suggest taking a look at the biomaRt vignette (https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html) and seeing if you can run any of the examples in there. If that code works for you then the issue probably lies with GEDI. If you still get errors then it's a biomaRt issue and I might be able to help more.

I'd suggest running Section 2 in that vignette, and then trying some of the examples in section 6. You should be able to copy and paste the code and get back the same results you see in that document. If you get some errors, please report them here.

Maryan12m commented 1 year ago

HI Mike Smith, The problem was fixed. thanks a lot

But I have a question about probe IDs: How do I convert agilent data probe IDs to Ensemble IDs via BiomaRt? I did easily for Affymetrix data but for agilent data there is no filter and attribute for Bovine species that I can use in BiomaRt. Should this be done by using the annotation file that exists on the GEO site using platform information through joining in Linux? Also, is it possible to merge 3 types of RNAseq, Affymetrix and Agilent data through Ensemble IDs through BiomaRt? The annotation file is attached.

Below is a part of the code for humans, but I don't know what I should choose in the attribute and filter section for the cow species: library(biomaRt) ensembl <- useMart('ensembl', dataset = ' btaurus_gene_ensemb') annot <- getBM( attributes = c('agilent_wholegenome', 'wikigene_description', 'ensembl_gene_id', 'entrezgene_id', 'gene_biotype', 'external_gene_name'), filters = 'agilent_wholegenome', values = probes, mart = ensembl).

Please advise. Thank you very much. GPL11649-18754.txt