Question: scan error in biomaRt with non-Ensemble datsets
0
gravatar for Rebecca
4 weeks ago by
Rebecca0
Rebecca0 wrote:

Hi all,

I am facing a scan error when using getBM with a mart that is not ensembl. The code below worked fine like a year or two ago, but I recently figured that it stopped doing that (I was upgrading my OS and R in between). Unfortunately, I don't know how to handle the error, the Mart object looks fine. Help is much appreciated!

Thanks a ton, Rebecca

> listMarts(host="biomart.vectorbase.org")
            biomart               version
1 vb_gene_mart_1908      VectorBase Genes
2        expression VectorBase Expression
>mart=listMarts(host="biomart.vectorbase.org")[1,1]

>VB=useMart(host="http://biomart.vectorbase.org", biomart=mart)
> VB
Object of class 'Mart':
  Using the vb_gene_mart_1908 BioMart database
  No dataset selected.

> Aed=useDataset(VB, dataset = "alvpagwg_eg_gene")
> Aed
Object of class 'Mart':
  Using the vb_gene_mart_1908 BioMart database
  Using the alvpagwg_eg_gene dataset

>getBM(attributes = "ensembl_gene_id",  mart = Aed, uniqueRows = TRUE) 
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 1 did not have 3 elements

I don't have these problems when I pick for example the Drosophila dataset from Ensembl.

Session:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=de_DE.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] biomaRt_2.40.4  magrittr_1.5    forcats_0.4.0   stringr_1.4.0   dplyr_0.8.3     purrr_0.3.2     readr_1.3.1     tidyr_0.8.3     tibble_2.1.3   
[10] ggplot2_3.2.1   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] progress_1.2.2       tidyselect_0.2.5     xfun_0.9             haven_2.1.1          lattice_0.20-38      colorspace_1.4-1     vctrs_0.2.0         
 [8] generics_0.0.2       stats4_3.6.1         blob_1.2.0           XML_3.98-1.20        rlang_0.4.0          pillar_1.4.2         glue_1.3.1          
[15] withr_2.1.2          DBI_1.0.0            BiocGenerics_0.30.0  bit64_0.9-7          modelr_0.1.5         readxl_1.3.1         munsell_0.5.0       
[22] gtable_0.3.0         cellranger_1.1.0     rvest_0.3.4          memoise_1.1.0        Biobase_2.44.0       knitr_1.24           IRanges_2.18.1      
[29] curl_4.0             parallel_3.6.1       AnnotationDbi_1.46.0 broom_0.5.2          Rcpp_1.0.2           scales_1.0.0         backports_1.1.4     
[36] S4Vectors_0.22.0     jsonlite_1.6         bit_1.1-14           digest_0.6.20        hms_0.5.0            stringi_1.4.3        grid_3.6.1          
[43] cli_1.1.0            tools_3.6.1          bitops_1.0-6         lazyeval_0.2.2       RCurl_1.95-4.12      RSQLite_2.1.2        crayon_1.3.4        
[50] pkgconfig_2.0.2      zeallot_0.1.0        prettyunits_1.0.2    xml2_1.2.2           lubridate_1.7.4      assertthat_0.2.1     httr_1.4.1          
[57] rstudioapi_0.10      R6_2.4.0             nlme_3.1-141         compiler_3.6.1      
software error • 54 views
ADD COMMENTlink modified 4 weeks ago by Mike Smith4.0k • written 4 weeks ago by Rebecca0
Answer: scan error in biomaRt with non-Ensemble datsets
0
gravatar for Mike Smith
4 weeks ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

It looks like VectorBase automatically redirects you to the https version of their site. biomaRt should be able to cope with this, but clearly it doesn't, so we'll have to be explicit. Try this for setting the mart host:

VB = useMart(host = "https://biomart.vectorbase.org", biomart = mart, port = 443)

I'll try to track down why biomaRt doesn't work this out for itself.

ADD COMMENTlink written 4 weeks ago by Mike Smith4.0k

Thanks a ton! It is working again!

ADD REPLYlink written 21 days ago by Rebecca0
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