[BioC] Understanding the randomness of Biomart
Nathan Harmston
iwanttobeabadger at googlemail.com
Sun Aug 17 21:23:42 CEST 2008
Hi everyone,
I have been playing with the biomaRt package a bit more and I am
trying to work out what is going on here:
ensembl = useMart("ensembl_mart_47", dataset =
"hsapiens_gene_ensembl", archive = TRUE)
fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters =
c("chromosome_name", "start", "end"), values = list(as.numeric("9"),
19198907, 19357826), mart = ensembl)
affy_hg_u133_plus_2 hgnc_symbol
1 226867_at
2 205684_s_at
3 226867_at DENND4C
4 205684_s_at DENND4C
5 234968_at
6 234968_at DENND4C
fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters =
c("chromosome_name", "start", "end"), values = list(as.numeric("9"),
33925736, 34088257), mart = ensembl)
affy_hg_u133_plus_2 hgnc_symbol
1
2 224789_at
3 224789_at WDR40A
I cannot understand why I am getting 2 rows for some probesets one
containing a hugo identifier and the other not? And whether there is
any relevance to this result ( probeset 234968_at ) and why I have
some results which don't show any probeset at all? Is there a specific
reason for this or is this just a something that needs to be post
filtered?
Many thanks in advance.
Nathan
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