error when connecting to BioMart about honeybadger

[JEFworks]

Hi Haoteng,

It looks like BioMart may just have been temporarily down or the proxy that is used in the tutorial may have been down. I just tried and it seems like BioMart is back up. Please try again.

You can always try a different host if it's a host-specific issue: https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html
As you've seen from the tutorial, HoneyBADGER uses the BioMart object to pull out each gene's chromosome, start, and end positions that's in your expression matrix. If you want to combine with the allele-based model, the coordinates of these start and end positions will need to match up so you will want to make sure the human reference genome version from BioMart matches the one you used for your alignment.

Hope that helps,
Jean

[HaotengYan]

Thank you for your kindly reply. This problem seems to be solved.