User: EdgeR_A_Poe

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EdgeR_A_Poe10
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Posts by EdgeR_A_Poe

<prev • 4 results • page 1 of 1 • next >
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Comment: C: biomaRt: Ensembl -> Entrez conversion error?
... Thanks again, Mike,  Yeah, I think dplyr::left_join() would have been helpful here. And you're correct - removing the version number from those failed genes and re-running biomaRt with the filter ensembl_gene_id  worked.  ...
written 7 months ago by EdgeR_A_Poe10
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Comment: C: biomaRt: Ensembl -> Entrez conversion error?
... Hi Mike,  Thanks for your response. Any insight about biomaRt dropping lines containing Ensembl IDs it doesn't recognize? I double checked to make sure the list going in was the correct length but the output is missing several lines. This is what caused a frame shift in my dataset and messed up the ...
written 7 months ago by EdgeR_A_Poe10
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Comment: C: biomaRt: Ensembl -> Entrez conversion error?
... Hi James,  You're correct about the IDs being unordered. I was re-ordering them in Excel so that the DE information (F value, P-Value, etc.) was correctly lined up. What I discovered is that in some cases, instead of returning an "NA" for Ensembl IDs it doesn't recognize, it will occasionally just ...
written 7 months ago by EdgeR_A_Poe10
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biomaRt: Ensembl -> Entrez conversion error?
... Prior to doing GO term enrichment analysis, I've been trying to convert the Ensembl IDs of differentially expressed genes to Entrez IDs using the R package biomaRt. I've done some spot checking and it looks like everything is getting converted correctly. However, I've run into two particular Ensembl ...
biomart ensembl entrez gene identifiers conversion written 7 months ago by EdgeR_A_Poe10 • updated 7 months ago by Mike Smith3.8k

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