Problem with ViSEAGO: 'Unexpected format to the list of available marts'
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Rachel • 0
@3b1105c9
Last seen 2.1 years ago
United Kingdom

Hello, I am having trouble with loading the ensembl mart as part of the viseago package. This worked earlier on this morning, so I am not sure what is wrong.

this is the code that no longer works


> # merge results from topGO
> BP_sResults <- ViSEAGO::merge_enrich_terms(
+   Input=list(
+     hSkMC_Low = c("MC_BP2", "MC_classic2"),
+     hSkMC_High = c("MC_BP", "MC_classic"),
+     hSkMC_CDK4_hTERT_Low = c("CH_BP2", "CH_classic2"),
+     hSkMC_CDK4_hTERT_High = c("CH_BP", "CH_classic"),
+     HeLa_Low = c("HL_BP2", "HL_classic2"),
+     HeLa_High = c("HL_BP", "HL_classic")
+   )
+ )

Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
https://apr2022.archive.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt
ViSEAGO • 554 views
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Is this still a problem? This code now seems to work for me. Ensembl was updated to version 106 in the last few days, and it may have been that you hit it when it wasn't quite ready.

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