Hello,
I am trying to get information on a probes from the
illumina_humanwg_6_v1 platform using the R interface with the biomaRt
library. For some reason, some probes (around 1500) seem to no longer have
any information on ensembl.
For example, "0004730161" is a probe with
no information through this interface,
>
getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"),
filters="illumina_humanwg_6_v1", values=c("0004730161"), uniqueRows=TRUE,
mart=ensembl)
[1] illumina_humanwg_6_v1 hgnc_symbol entrezgene
(or
0-length row.names)
where as, "0006980528" is a probe that has
information
> getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol",
"entrezgene"), filters="illumina_humanwg_6_v1", values=c("0006980528"),
uniqueRows=TRUE, mart=ensembl)
illumina_humanwg_6_v1 hgnc_symbol
entrezgene
1 6980528 ATP10D 57205 The BioMart web interface on the
ensembl website however does provide information for both these probes. I
am at a loss at trying to explain the missing probes from the biomaRt R
interface. Any help would be greatly appreciated. Thanks, Reuben Thomas _______________________________________________
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