Question: biomart not ound some prevous release
0
gravatar for jarod_v6@libero.it
6 months ago by
Italy
jarod_v6@libero.it40 wrote:

Dear all, I need to annotate some rnaseq data from human. I use ensemble 74. On biomart I'm not able to found? It is normal? Why?

 listEnsemblArchives()
             name     date                                url
1  Ensembl GRCh37 Feb 2014          http://grch37.ensembl.org
2      Ensembl 95 Jan 2019 http://jan2019.archive.ensembl.org
3      Ensembl 94 Oct 2018 http://oct2018.archive.ensembl.org
4      Ensembl 93 Jul 2018 http://jul2018.archive.ensembl.org
5      Ensembl 92 Apr 2018 http://apr2018.archive.ensembl.org
6      Ensembl 91 Dec 2017 http://dec2017.archive.ensembl.org
7      Ensembl 90 Aug 2017 http://aug2017.archive.ensembl.org
8      Ensembl 89 May 2017 http://may2017.archive.ensembl.org
9      Ensembl 88 Mar 2017 http://mar2017.archive.ensembl.org
10     Ensembl 87 Dec 2016 http://dec2016.archive.ensembl.org
11     Ensembl 86 Oct 2016 http://oct2016.archive.ensembl.org
12     Ensembl 85 Jul 2016 http://jul2016.archive.ensembl.org
13     Ensembl 84 Mar 2016 http://mar2016.archive.ensembl.org
14     Ensembl 83 Dec 2015 http://dec2015.archive.ensembl.org
15     Ensembl 82 Sep 2015 http://sep2015.archive.ensembl.org
16     Ensembl 81 Jul 2015 http://jul2015.archive.ensembl.org
17     Ensembl 80 May 2015 http://may2015.archive.ensembl.org
18     Ensembl 79 Mar 2015 http://mar2015.archive.ensembl.org
19     Ensembl 78 Dec 2014 http://dec2014.archive.ensembl.org
20     Ensembl 77 Oct 2014 http://oct2014.archive.ensembl.org
21     Ensembl 76 Aug 2014 http://aug2014.archive.ensembl.org
22     Ensembl 75 Feb 2014 http://feb2014.archive.ensembl.org
23     Ensembl 67 May 2012 http://may2012.archive.ensembl.org
24     Ensembl 54 May 2009 http://may2009.archive.ensembl.org
   version current_release
1   GRCh37                
2       95               *
3       94                
4       93                
5       92                
6       91                
7       90                
8       89                
9       88                
10      87                
11      86                
12      85                
13      84                
14      83                
15      82                
16      81                
17      80                
18      79                
19      78                
20      77                
21      76                
22      75                
23      67                
24      54  


> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 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_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] genefilter_1.64.0           limma_3.38.3               
 [3] biomaRt_2.38.0              reshape2_1.4.3             
 [5] RColorBrewer_1.1-2          ggplot2_3.1.0              
 [7] pheatmap_1.0.10             DESeq2_1.22.1              
 [9] SummarizedExperiment_1.12.0 DelayedArray_0.8.0         
[11] BiocParallel_1.16.2         matrixStats_0.54.0         
[13] Biobase_2.42.0              GenomicRanges_1.34.0       
[15] GenomeInfoDb_1.18.1         IRanges_2.16.0             
[17] S4Vectors_0.20.1            BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
 [1] httr_1.4.0             bit64_0.9-7           
 [3] splines_3.5.2          Formula_1.2-3         
 [5] assertthat_0.2.0       latticeExtra_0.6-28   
 [7] blob_1.1.1             GenomeInfoDbData_1.2.0
 [9] progress_1.2.0         yaml_2.2.0            
[11] pillar_1.3.1           RSQLite_2.1.1         
[13] backports_1.1.3        lattice_0.20-38       
[15] glue_1.3.0             digest_0.6.18         
[17] XVector_0.22.0         checkmate_1.8.5       
[19] colorspace_1.3-2       htmltools_0.3.6       
[21] Matrix_1.2-15          plyr_1.8.4            
[23] XML_3.98-1.16          pkgconfig_2.0.2       
[25] zlibbioc_1.28.0        purrr_0.2.5           
[27] xtable_1.8-3           scales_1.0.0          
[29] htmlTable_1.12         tibble_1.4.2          
[31] annotate_1.60.0        withr_2.1.2           
[33] nnet_7.3-12            lazyeval_0.2.1        
[35] survival_2.43-3        magrittr_1.5          
[37] crayon_1.3.4           memoise_1.1.0         
[39] foreign_0.8-71         prettyunits_1.0.2     
[41] tools_3.5.2            data.table_1.11.8     
[43] hms_0.4.2              stringr_1.3.1         
[45] locfit_1.5-9.1         munsell_0.5.0         
[47] cluster_2.0.7-1        AnnotationDbi_1.44.0  
[49] bindrcpp_0.2.2         compiler_3.5.2        
[51] rlang_0.3.0.1          grid_3.5.2            
[53] RCurl_1.95-4.11        rstudioapi_0.8        
[55] htmlwidgets_1.3        bitops_1.0-6          
[57] base64enc_0.1-3        gtable_0.2.0          
[59] curl_3.2               DBI_1.0.0             
[61] R6_2.3.0               gridExtra_2.3         
[63] knitr_1.21             dplyr_0.7.8           
[65] bit_1.1-14             bindr_0.1.1           
[67] Hmisc_4.1-1            stringi_1.2.4         
[69] Rcpp_1.0.0             geneplotter_1.60.0    
[71] rpart_4.1-13           acepack_1.4.1         
[73] tidyselect_0.2.5       xfun_0.4
rnaseq biomart • 127 views
ADD COMMENTlink modified 6 months ago by Mike Smith3.9k • written 6 months ago by jarod_v6@libero.it40
Answer: biomart not ound some prevous release
0
gravatar for Mike Smith
6 months ago by
Mike Smith3.9k
EMBL Heidelberg / de.NBI
Mike Smith3.9k wrote:

biomaRt lists the Ensembl archives found at http://www.ensembl.org/info/website/archives/index.html If the version that you want is not found there, then it has probably been permanently retired by Ensembl. You can try to contact them to see if you can obtain an offline version of the annotation, but it is unlikely that it made available via the biomaRt interface again.

ADD COMMENTlink written 6 months ago by Mike Smith3.9k
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