Recent problem with biomaRt query
Entering edit mode
nickp60 • 0
Last seen 5.9 years ago
United States

Has anyone run into issues recently with sumitting biomaRt queries?  I am submitting a list of bacterial gene accessions to uniprot dataset and returning GO ID's.  Last month, with the same list of ~384 genes, I was returning a list of about 500 GO Terms.  Now, I get around 250 GO Terms. Was there an update that I missed, or can anyone suggest an alternate explanation?




R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)

[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] grid      parallel  stats4    stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
 [1] RCurl_1.95-4.6            bitops_1.0-6              gridExtra_0.9.1          
 [4] fpc_2.1-9                 e1071_1.6-4               plyr_1.8.2               
 [7] biomaRt_2.24.0            reshape2_1.4.1            shiny_0.12.0             
[10] DESeq2_1.8.1              RcppArmadillo_0. Rcpp_0.11.6              
[13] GenomicRanges_1.20.3      GenomeInfoDb_1.4.0        IRanges_2.2.1            
[16] S4Vectors_0.6.0           BiocGenerics_0.14.0       ggplot2_1.0.1            
[19] XLConnect_0.2-11          XLConnectJars_0.2-9       dplyr_0.4.1              

loaded via a namespace (and not attached):
 [1] Biobase_2.28.0       jsonlite_0.9.16      splines_3.2.0       
 [4] Formula_1.2-1        assertthat_0.1       latticeExtra_0.6-26 
 [7] robustbase_0.92-3    RSQLite_1.0.0        lattice_0.20-31     
[10] digest_0.6.8         RColorBrewer_1.1-2   XVector_0.8.0       
[13] colorspace_1.2-6     htmltools_0.2.6      httpuv_1.3.2        
[16] XML_3.98-1.1         genefilter_1.50.0    xtable_1.7-4        
[19] mvtnorm_1.0-2        scales_0.2.4         BiocParallel_1.2.1  
[22] annotate_1.46.0      nnet_7.3-9           lazyeval_0.1.10     
[25] proto_0.3-10         survival_2.38-1      magrittr_1.5        
[28] mime_0.3             mclust_5.0.1         MASS_7.3-40         
[31] foreign_0.8-63       class_7.3-12         tools_3.2.0         
[34] trimcluster_0.1-2    stringr_1.0.0        kernlab_0.9-20      
[37] munsell_0.4.2        locfit_1.5-9.1       cluster_2.0.1       
[40] AnnotationDbi_1.30.1 lambda.r_1.1.7       futile.logger_1.4.1 
[43] labeling_0.3         gtable_0.1.2         flexmix_2.3-13      
[46] DBI_0.3.1            R6_2.0.1             prabclus_2.2-6      
[49] Hmisc_3.16-0         futile.options_1.0.0 modeltools_0.2-21   
[52] rJava_0.9-6          stringi_0.4-1        geneplotter_1.46.0  
[55] rpart_4.1-9          acepack_1.3-3.3      DEoptimR_1.0-2      
[58] diptest_0.75-6      

biomart biomaRt R rstudio • 664 views
Entering edit mode
nickp60 • 0
Last seen 5.9 years ago
United States

A little more digging reveals that the database I have been using had been part of a proteome culling effort to reduce redundency.  See the link below for more info.


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