Question: listDatasets(ensembl) displays strange behavior + scerevisiae_gene_ensembl not available on biomaRt?
1
gravatar for Emmanuel Levy
22 months 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   

 

biomart bioconductor • 717 views
ADD COMMENTlink modified 22 months ago • written 22 months 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 22 months ago by igor30

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

BiocInstaller::biocLite('biomaRt')
ADD REPLYlink written 22 months ago by Mike Smith4.0k
Answer: listDatasets(ensembl) displays strange behavior + scerevisiae_gene_ensembl not a
1
gravatar for Emmanuel Levy
22 months 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 22 months 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 22 months ago • written 22 months ago by Mike Smith4.0k
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