Is the hgu133plus2.db annotation package outdated ?
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@matheuscburger-9229
Last seen 6.1 years ago
Brazil/São Paulo/ USP

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

hgu133plus2.db • 891 views
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@matheuscburger-9229
Last seen 6.1 years ago
Brazil/São Paulo/ USP

I already understood why this happens.

Question about mget vs. select for annotation package

Thank you

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