[BioC] Understanding the randomness of Biomart

[Nathan Harmston]

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