Error getLDS() - Error in attributes(.Data)

[saphir746]

trying to do the following and it's not working,

please send suggestions

`myList<-c("ATP5F1A" "ATP5F1B" "ATP5F1C" ) require("biomaRt") human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl") genesV2 = getLDS(attributes = c("hgnc_symbol"), filters = "hgnc_symbol", values = myList , mart = human, attributesL = c("mgi_symbol"), martL = mouse, uniqueRows=T)

Error in attributes(.Data) <- c(attributes(.Data), attrib) : 'names' attribute [2] must be the same length as the vector [1] `

[grimbough]

Thanks for reporting this and providing the code. I currently get a slightly different error:

myList<-c("ATP5F1A", "ATP5F1B", "ATP5F1C" )
library("biomaRt")
human <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl", mirror = "uswest")
mouse <- useEnsembl("ensembl", dataset = "mmusculus_gene_ensembl", mirror = "uswest")
genesV2 = getLDS(attributes = c("hgnc_symbol"), 
                 filters = "hgnc_symbol", 
                 values = myList , 
                 mart = human, 
                 attributesL = c("mgi_symbol"), 
                 martL = mouse, uniqueRows=T)
#> Error: biomaRt has encountered an unknown server error. HTTP error code: 502
#> Please report this on the Bioconductor support site at https://support.bioconductor.org/
#> Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

I think is a continuation of the problems Ensembl BioMart is having with the linked dataset queries, which people have been reporting ever since the release of Ensembl 106 (#61, #63, #59) and unfortunately doesn't seem to be fixed yet.

One option is to use the version 105 archive e.g.

human <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl", version = 105)
mouse <- useEnsembl("ensembl", dataset = "mmusculus_gene_ensembl", version = 105)
genesV2 = getLDS(attributes = c("hgnc_symbol"), 
                 filters = "hgnc_symbol", 
                 values = myList , 
                 mart = human, 
                 attributesL = c("mgi_symbol"), 
                 martL = mouse, uniqueRows=T)
genesV2
#>   HGNC.symbol MGI.symbol
#> 1     ATP5F1A     Atp5a1
#> 2     ATP5F1B      Atp5b
#> 3     ATP5F1C     Atp5c1

[Shicheng-Guo]

Same issue. any solution comes out?

[pratarora]

Same issue. any solution yet?

[JohnGenome]

It seems that useMart() can only use Ensembl 109, while useEnsembl() can use previous versions. I tried many versions and find only Ensembl 105 works well. So this problem can be solved by adding Ensembl version 105 to the useEnsembl() as grimbough suggested.

[rbutleriii]

Still occurring, for fixed version specification. If I use:

  mouse = useEnsembl("ensembl", dataset="mmusculus_gene_ensembl", version="105")
  human = useEnsembl("ensembl", dataset="hsapiens_gene_ensembl", version="105")
  # match with ensembl_gene_id across both
  x = data.table(getLDS(mart=mouse, attributes=c('ensembl_gene_id'), martL=human,
                        attributesL=c('ensembl_gene_id', 'chromosome_name', 
                                      'gene_biotype'), 
                        filters='ensembl_gene_id', values=unique(dt[[colname]]),
                        bmHeader=F))

It will work, but version=110, 109, etc same error. If I specify no version or mirror, I get:

Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
Ensembl site unresponsive, trying uswest mirror
Error in .chooseEnsemblMirror(mirror = mirror, httr_config = httr_config) :
  Unable to query any Ensembl site