[biomart-users] query to the BioMart webservice returned an invalid result

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LA
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[biomart-users] query to the BioMart webservice returned an invalid result

LA
I received the following result running biomaRt:

> library(biomaRt)
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl)
+
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> getBM(attributes=c("ensembl_transcript_id","ensembl_gene_id"),filters="ensembl_gene_id",mart=ensembl,values="ENSG00000196182")
Error in getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id"),  :
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.34.2

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Re: [biomart-users] query to the BioMart webservice returned an invalid result

Steffen Durinck-2
Hi Lynn,

Looks like a temporary glitch, try again and it should work.
It works for me.

Best,
Steffen

On Mon, Apr 23, 2018 at 9:53 AM, LA <[hidden email]> wrote:
I received the following result running biomaRt:

> library(biomaRt)
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl)
+
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> getBM(attributes=c("ensembl_transcript_id","ensembl_gene_id"),filters="ensembl_gene_id",mart=ensembl,values="ENSG00000196182")
Error in getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id"),  :
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.34.2

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LA
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Re: [biomart-users] query to the BioMart webservice returned an invalid result

LA
Thanks for responding, Steffen. I am still having the same problem. Are you using a different host? 

On Mon, Apr 23, 2018 at 11:28 AM, Steffen Durinck <[hidden email]> wrote:
Hi Lynn,

Looks like a temporary glitch, try again and it should work.
It works for me.

Best,
Steffen

On Mon, Apr 23, 2018 at 9:53 AM, LA <[hidden email]> wrote:
I received the following result running biomaRt:

> library(biomaRt)
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl)
+
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> getBM(attributes=c("ensembl_transcript_id","ensembl_gene_id"),filters="ensembl_gene_id",mart=ensembl,values="ENSG00000196182")
Error in getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id"),  :
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.34.2

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