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Hi
I am using mouse4302 chips and my biology counterpart found some odds
annotations,
for a non negligible number of gene the symbols produced by
Bioconductor and affymetrix web site
are very different (meaning they are even not synonyms), usually what
it happens is that
the genes are next to each other in the genome (If you look at them
in USCS genome browser)
An example
probeset: 1442021_at:
Bioconductor annotation
entrez id: 225651 symbol:Mppe1
refseq: NM_172630 NP_766218 XM_001001173 XM_001001180
XM_001001193 XM_001001206 XM_001001219 XP_001001173
XP_001001180 XP_001001193 XP_001001206 XP_001001219
Affy annotation
entrez id: 14680 symbol: Gnal
refseq: NM_010307 NM_177137
I guess my question is how is the mapping done, so that it results in
such a difference...and which one
is better. For what reason are those annotation at odds with
affymetrix. Which at should believe better ?
Thanks in advance
Mayte