Hi,
I usually retrieve the annotation of a probe in this way:
library(hgu133plus2.db)
mget(c('214657_s_at', '224565_at', '224566_at'), hgu133plus2ENTREZID)
# $`214657_s_at`
# [1] NA
#
# $`224565_at`
# [1] NA
#
# $`224566_at`
# [1] NA
These probes does not have an annotation, right ?
But today I tried to look at NCBI GEO annotation (GPL570). I did a simple grep on the file ...
grep '214657_s_at' GPL570-13270.txt
# 214657_s_at AU134977 Homo sapiens Jun 9, 2011 Consensus sequence GenBank gb:AU134977 /DB_XREF=gi:10995516 /DB_XREF=AU134977 /CLONE=PLACE1000926 /FEA=mRNA /CNT=172 /TID=Hs.322149.0 /TIER=ConsEnd /STK=0 /UG=Hs.322149 /UG_TITLE=Human clone 137308 mRNA, partial cds AU134977 nuclear paraspeckle assembly transcript 1 (non-protein coding) NEAT1 283131 NR_028272
grep '224565_at' GPL570-13270.txt
# 224565_at BE675516 Homo sapiens Jun 9, 2011 Consensus sequence GenBank gb:BE675516 /DB_XREF=gi:10036057 /DB_XREF=7f10f01.x1 /CLONE=IMAGE:3294265 /FEA=mRNA /CNT=440 /TID=Hs.240443.0 /TIER=Stack /STK=15 /UG=Hs.240443 /UG_TITLE=Homo sapiens cDNA: FLJ23538 fis, clone LNG08010, highly similar to BETA2 Human MEN1 region clone epsilonbeta mRNA BE675516 nuclear paraspeckle assembly transcript 1 (non-protein coding) NEAT1 283131 NR_028272
grep '224566_at' GPL570-13270.txt
# 224566_at AI042152 Homo sapiens Jun 9, 2011 Consensus sequence GenBank gb:AI042152 /DB_XREF=gi:3281346 /DB_XREF=oy37a06.x1 /CLONE=IMAGE:1667986 /FEA=mRNA /CNT=440 /TID=Hs.240443.0 /TIER=Stack /STK=22 /UG=Hs.240443 /UG_TITLE=Homo sapiens cDNA: FLJ23538 fis, clone LNG08010, highly similar to BETA2 Human MEN1 region clone epsilonbeta mRNA AI042152 nuclear paraspeckle assembly transcript 1 (non-protein coding) NEAT1 283131 NR_028272
These three probes were annotated on "Jun 9, 2011" as NEAT1.
Could someone help me to understand why there is such difference between NCBI/GEO and bioconductor ?
Thanks,
Matheus
