Entering edit mode
All,
I understand the concept of multiple probesets corresponding to one
identifier. But what is the meaning of
a probeset corresponding to multiple identifiers? And below, given
that 220547_s_at has a match,
why should another row be returned with NA.
Did I happen to choose a few probesets where the gene definition is
changing, or am I misunderstanding
something else, such as the biomart syntax.
Thanks,
Juliet
library("biomaRt")
probeSets <- c("219666_at", "220547_s_at", "218034_at")
ensembl = useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
getBM(attributes = c("affy_hg_u133a", "entrezgene"), filters =
"affy_hg_u133a",values = probeSets, mart = ensembl)
affy_hg_u133a entrezgene
1 220547_s_at 54537
2 218034_at 51024
3 220547_s_at NA
4 219666_at 64231
5 220547_s_at 414241
6 220547_s_at 439965
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.12.0 BiocInstaller_1.4.6
loaded via a namespace (and not attached):
[1] RCurl_1.91-1 tools_2.15.0 XML_3.9-4
