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Question: listDatasets(ensembl) displays strange behavior + scerevisiae_gene_ensembl not available on biomaRt?
1
gravatar for Emmanuel Levy
4 weeks ago by
Emmanuel Levy270
Emmanuel Levy270 wrote:

Hi All,

 

I have been trying to connect to the scerevisiae dataset using biomart and I cannot. I wonder if it's me or a more general problem.

 

I also notive a very strange behavior with listDatasets, which returns different output when it's called multiple times.

 

ensembl=useMart("ensembl")
listDatasets(ensembl)

 

--> returns 34 datasets, another time 51, another time 48 ...

 

hsapiens = useMart("ensembl", dataset="hsapiens_gene_ensembl")

Works fine, but ....

 

yeast = useMart("ensembl", dataset="scerevisiae_gene_ensembl")
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  scerevisiae_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.

 

In addition, listDatasets exhibit a very strange behavior: caling it multiple times returns a different output each time:

> dim(listDatasets(ensembl))
[1] 51  3
> dim(listDatasets(ensembl))
[1] 48  3
> dim(listDatasets(ensembl))
[1] 34  3
> dim(listDatasets(ensembl))
[1] 48  3
> dim(listDatasets(ensembl))
[1] 34  3​

 

If anyone has a clue for how to fix this I'd be happy to know.

 

Thank you,

 

Emmanuel

 

 

> sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X Yosemite 10.10.5


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     


other attached packages:

[1] biomaRt_2.30.0


loaded via a namespace (and not attached):

 [1] Rcpp_0.12.14         IRanges_2.8.2        XML_3.98-1.9         digest_0.6.12        bitops_1.0-6        

 [6] DBI_0.7              stats4_3.3.3         RSQLite_2.0          rlang_0.1.4          blob_1.1.0          

[11] S4Vectors_0.12.2     tools_3.3.3          bit64_0.9-7          Biobase_2.34.0       RCurl_1.95-4.8      

[16] bit_1.1-12           parallel_3.3.3       BiocGenerics_0.20.0  AnnotationDbi_1.36.2 memoise_1.1.0       

[21] tibble_1.3.4   

 

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Emmanuel Levy270

I am also having the same problem with listDatasets() returning a different output every time. Very strange behavior.

ADD REPLYlink written 4 weeks ago by igor20

Please try updating your version of biomaRt to 2.34.1 or newer.  You can do this via:

BiocInstaller::biocLite('biomaRt')
ADD REPLYlink written 4 weeks ago by Mike Smith2.2k
1
gravatar for Emmanuel Levy
4 weeks ago by
Emmanuel Levy270
Emmanuel Levy270 wrote:

Running the following command, as suggested in a previous post seems to have fixed those issues:

BiocInstaller::biocLite('grimbough/biomaRt')

 

 
ADD COMMENTlink written 4 weeks ago by Emmanuel Levy270
1

Just adding that the required changes to biomaRt have now propagated into the versions available via Bioconductor, so you can also use the normal installation command:

BiocInstaller::biocLite('biomaRt')

 

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Mike Smith2.2k
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