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LauraPS1 / TFEA.ChIP_downloads

TFEA.ChIP is an R package in developement. Its purpose is to analyze transcription factor enrichment in a set of differentially expressed genes.
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preProcessInputData + geneIDtoEntrez #3

Closed reberya closed 1 year ago

reberya commented 4 years ago

Hello,

The preProcessInputData needs to be updated with its use of ensembl's biomart. Some of the terms have changed. The example I ran into was that "Entrezgene" is now entrezgene_id. When running the preProcessInput function returns an error that it cannot get the attribute from biomaRt and asks user to find proper attribute using listAttributes().

LauraPS1 commented 4 years ago

Hello reverya, What version of the package are you using? This was corrected roughly when biomaRt's terminology changed and neither the source package in this repository nor the version available via Bioconductor use "Entrezgene".

If the error persists after updating the package, please post a snippet of the code you used and the error message returned.

Cheers.