Off topic:Need Ensembl transcripts detected by Illumina_humanht_12_v4 probes
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@charkerrhodes-9364
Last seen 8.3 years ago
United States

I need a table listing the Ensembl transcripts detected by each of the Illumina_humanht_12_v4 probes When I give the obvious getBM() command to use  R to get the data from BioMart (see code below) I get a table containing only about ¾ of the Illumina probes.

In the example below, I attempt to download the Ensembl transcripts for two  Illumina_humanht_12_v4 probes;  the first probe is recognized and the transcript returned, but the second is not. 

This is a more general formulation of my post yesterday "Can't match on some, but not all, Illumina probe IDs using biomaRt".  If someone can tell me what's wrong with the code below, that would be nice, but what I actually need is a table listing the Ensembl transcripts detected by each of the Illumina_humanht_12_v4 probes – It doesn't have to come from BioMart if there is some other place I can get it.

> library(biomaRt)
> ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host='www.ensembl.org')

> getBM(attributes=c("illumina_humanht_12_v4", "hgnc_symbol", "ensembl_transcript_id"), 
+       filters = "illumina_humanht_12_v4", 
+       values = "ILMN_1789991",
+       mart = ensembl)
  illumina_humanht_12_v4 hgnc_symbol ensembl_transcript_id
1           ILMN_1789991      MARCH4       ENST00000273067

> getBM(attributes=c("illumina_humanht_12_v4", "hgnc_symbol", "ensembl_transcript_id"), 
+       filters = "illumina_humanht_12_v4", 
+       values = "ILMN_1735038",
+       mart = ensembl)
[1] illumina_humanht_12_v4 hgnc_symbol            ensembl_transcript_id 
<0 rows> (or 0-length row.names)

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] biomaRt_2.26.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.4        parallel_3.2.2       DBI_0.3.1           
 [4] RCurl_1.95-4.7       Biobase_2.30.0       AnnotationDbi_1.32.0
 [7] RSQLite_1.0.0        S4Vectors_0.8.3      BiocGenerics_0.16.1 
[10] stats4_3.2.2         bitops_1.0-6         XML_3.98-1.3 

Illumina_humanht_12_v4 probes ensembl biomart bioconductor • 727 views
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