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lgatto / pRoloc

A unifying bioinformatics framework for organelle proteomics
http://lgatto.github.io/pRoloc/
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Biomart error - can not set params #66

Closed lmsimp closed 8 years ago

lmsimp commented 8 years ago

I would like to select yeast and then Uniprot IDs to pull GO annotation for Dan's data.

I try:

params <- setAnnotationParams()
Select species 

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.
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171: Saccharomyces cerevisiae genes (R64-1-1)
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.
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 Selection: 171

Select filter 

 1: EMBL ID(s) [e.g. D87018]
 2: Ensembl exon ID(s) [e.g. ENSE00001508081]
 3: Ensembl Gene ID(s) [e.g. ENSG00000139618]
 4: Ensembl protein ID(s) [e.g. ENSP00000369497]
 5: Ensembl Transcript ID(s) [e.g. ENST00000380152]
 6: EntrezGene ID(s) [e.g. 115286]
 7: Protein (Genbank) ID(s) [e.g. BAA20017]
 8: Refseq DNA ID(s) [e.g. NM_203373]
 9: Refseq mRNA ID(s) [e.g. NM_001195597]
10: Refseq protein ID(s) [e.g. NP_001005353]
11: SGD Gene ID(s) [e.g. S000006365]
12: SGD Transcript ID(s) [e.g. S000006365]
13: UniProt/Swissprot ID(s) [e.g. Q13068]
14: UniProt/TrEMBL ID(s) [e.g. A2MYD1]
15: WikiGene ID(s) [e.g. 115286]
16: WikiGene Name(s) [e.g. SLC25A26]

Selection: 13
Connecting to Biomart...
Error in validMsg("Mart biomart slot and martname do not match.") : 
  argument "result" is missing, with no default

I get a similar message when I try with selecting 170: Saccharomyces cerevisiae genes (R64-1-1 (2011-11-SGD))

lgatto commented 8 years ago 
> library(pRoloc)
> p <- setAnnotationParams()
Select species 

  1: Acyrthosiphon pisum genes (Acyr_2.0 (AphidBase 2.1))
  2: Aedes aegypti genes (AaegL3 (AaegL3.3))
  3: Aegilops tauschii genes (ASM34733v1 (2013-12-BGI))
  4: Ailuropoda melanoleuca genes (ailMel1)
  5: Amborella trichopoda genes (AMTR1.0 (2014-01-AGD))
  6: Amphimedon queenslandica genes (Aqu1 (2010-10-JGI))
  7: Anas platyrhynchos genes (BGI_duck_1.0)
  8: Anolis carolinensis genes (AnoCar2.0)
  9: Anopheles darlingi genes (AdarC3 (AdarC3.2))
 10: Anopheles gambiae genes (AgamP4 (AgamP4.2))
...
167: Rattus norvegicus genes (Rnor_6.0)
168: Rhodnius prolixus genes (RproC1 (RproC1.3))
169: Saccharomyces cerevisiae genes (R64-1-1)
170: Saccharomyces cerevisiae genes (R64-1-1 (2011-11-SGD))
171: Sarcophilus harrisii genes (DEVIL7.0)
172: Schistosoma mansoni genes (ASM23792v2 (2012-04-GeneDB))
173: Schizosaccharomyces cryophilus genes (SCY4 (2013-08-Broad))
...
203: Tupaia belangeri genes (tupBel1)
204: Tursiops truncatus genes (turTru1)
205: Ustilago maydis genes (UM1 (2011-04-Broad))
206: Verticillium dahliae genes (ASM15067v1 (2011-09-Broad))
207: Verticillium dahliae JR2 genes (VDAG_JR2v.4.0 (2014-09-LPPWU))
208: Vicugna pacos genes (vicPac1)
209: Vitis vinifera genes (IGGP_12x (2012-07-CRIBI))
210: Xenopus tropicalis genes (JGI4.2)
211: Xiphophorus maculatus genes (Xipmac4.4.2)
212: Yarrowia lipolytica genes (ASM252v1 (2012-05-Genolevures))
213: Zea mays genes (AGPv3 (5b))
214: Zootermopsis nevadensis genes (ZooNev1.0 (2014-06-EnsemblMetazoa))
215: Zymoseptoria tritici genes (MG2 (2011-07-JGI))

Selection: 169
Select filter 

 1: EMBL ID(s) [e.g. AY495257]
 2: Ensembl exon ID(s) [e.g. ENSE00001508081]
 3: Ensembl Gene ID(s) [e.g. ENSG00000139618]
 4: Ensembl protein ID(s) [e.g. ENSP00000369497]
 5: Ensembl Transcript ID(s) [e.g. ENST00000380152]
 6: EntrezGene ID(s) [e.g. 115286]
 7: Protein (Genbank) ID(s) [e.g. ACU09872]
 8: RefSeq DNA ID(s) [e.g. NM_203373]
 9: RefSeq mRNA ID(s) [e.g. NM_001195597]
10: RefSeq protein ID(s) [e.g. NP_001005353]
11: SGD Gene ID(s) [e.g. S000006365]
12: SGD Transcript ID(s) [e.g. S000006365]
13: UniProt/Swissprot Accession(s) [e.g. Q13068]
14: UniProt/TrEMBL Accession(s) [e.g. U5Z754]
15: WikiGene ID(s) [e.g. 115286]
16: WikiGene Name(s) [e.g. SLC25A26]

Selection: 13
Connecting to Biomart...
> p
Object of class "AnnotationParams"
 Using the 'ENSEMBL_MART_ENSEMBL' BioMart database
 Using the 'scerevisiae_gene_ensembl' dataset
 Using 'uniprot_swissprot' as filter
 Created on Fri Dec 11 10:27:39 2015
> packageVersion("pRoloc")
[1] ‘1.11.2’
> sessionInfo()
R Under development (unstable) (2015-10-23 r69563)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

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

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] pRoloc_1.11.2        MLInterfaces_1.51.0  cluster_2.0.3       
 [4] annotate_1.49.0      XML_3.98-1.3         AnnotationDbi_1.33.1
 [7] IRanges_2.5.9        S4Vectors_0.9.11     MSnbase_1.19.4      
[10] ProtGenerics_1.3.3   BiocParallel_1.5.0   mzR_2.5.2           
[13] Rcpp_0.12.2          Biobase_2.31.1       BiocGenerics_0.17.2 
[16] biomaRt_2.27.2      

loaded via a namespace (and not attached):
 [1] nlme_3.1-122          pbkrtest_0.4-2        bitops_1.0-6         
 [4] doParallel_1.0.10     RColorBrewer_1.1-2    threejs_0.2.1        
 [7] prabclus_2.2-6        ggvis_0.4.2           tools_3.3.0          
[10] R6_2.1.1              affyio_1.41.0         rpart_4.1-10         
[13] mgcv_1.8-9            DBI_0.3.1             colorspace_1.2-6     
[16] trimcluster_0.1-2     nnet_7.3-11           gbm_2.1.1            
[19] compiler_3.3.0        preprocessCore_1.33.0 quantreg_5.19        
[22] SparseM_1.7           diptest_0.75-7        scales_0.3.0         
[25] sfsmisc_1.0-28        DEoptimR_1.0-4        mvtnorm_1.0-3        
[28] robustbase_0.92-5     randomForest_4.6-12   genefilter_1.53.0    
[31] affy_1.49.0           proxy_0.4-15          stringr_1.0.0        
[34] digest_0.6.8          minqa_1.2.4           base64enc_0.1-3      
[37] htmltools_0.2.6       lme4_1.1-10           rda_1.0.2-2          
[40] limma_3.27.6          htmlwidgets_0.5       RSQLite_1.0.0        
[43] impute_1.45.0         BiocInstaller_1.21.2  FNN_1.1              
[46] shiny_0.12.2          hwriter_1.3.2         mzID_1.9.0           
[49] mclust_5.1            gtools_3.5.0          car_2.1-0            
[52] dplyr_0.4.3           RCurl_1.95-4.7        magrittr_1.5         
[55] modeltools_0.2-21     Matrix_1.2-3          futile.logger_1.4.1  
[58] MALDIquant_1.14       munsell_0.4.2         proto_0.3-10         
[61] vsn_3.39.0            stringi_1.0-1         MASS_7.3-45          
[64] zlibbioc_1.17.0       flexmix_2.3-13        plyr_1.8.3           
[67] grid_3.3.0            pls_2.5-0             gdata_2.17.0         
[70] lattice_0.20-33       splines_3.3.0         knitr_1.11           
[73] fpc_2.1-10            lpSolve_5.6.13        reshape2_1.4.1       
[76] codetools_0.2-14      futile.options_1.0.0  pcaMethods_1.61.0    
[79] lambda.r_1.1.7        mlbench_2.1-1         nloptr_1.0.4         
[82] httpuv_1.3.3          foreach_1.4.3         MatrixModels_0.4-1   
[85] gtable_0.1.2          kernlab_0.9-22        assertthat_0.1       
[88] ggplot2_1.0.1         mime_0.4              xtable_1.8-0         
[91] e1071_1.6-7           class_7.3-14          survival_2.38-3      
[94] iterators_1.0.8       rgl_0.95.1367         caret_6.0-62         
[97] sampling_2.7