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Neurosurgery-Brain-Tumor-Center-DiazLab / CONICS

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
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Error in getGenePositions #40

Open TM9013 opened 2 years ago

TM9013 commented 2 years ago

Thanks for always providing us with useful tools. I am doing a tutorial on the glioblastoma demo data on your page.

I get an error at getGenePosition.

Here is my code and error display.

head(rownames(a)) [1] "1/2-SBSRNA4" "A1BG" "A1BG-AS1" "A1CF" "A2LD1" "A2M"

gene_pos=getGenePositions(rownames(a)) Error: Unexpected format to the list of available marts. Please check the following URL manually, and try ?listMarts for advice. http://dec2016.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

I tried linking to the given address and got the following message, which seems to be an error caused by the fact that the Ensembl Achives I am trying to reach are already unavailable.

image

Is there any way to work around this error?

Thanks in advance.

yanglq-bioinfo commented 1 year ago

may be you can try gene_pos <- getGenePositions(rownames(suva_expr),ensembl_version = "apr2022.archive.ensembl.org")