[BioC] problem with rat database

[Vincent Carey]

1) you did not provide sessionInfo(), which is critical for helping
you to diagnose an issue that may pertain to software version --
revisions to annotation packages can have all sorts of consequences

2) i am not sure rgug4130.db has anything to do with this.

> get("CB606456", revmap(rgug4130aSYMBOL))
Error in .checkKeys(value, Rkeys(x), x at ifnotfound) :
  value for "CB606456" not found


and so on.  look at the featureData component of the object passed to
lmFit -- the annotation may be in there.  if this does not give
clarification please give very explicity indication of how the
topTable was generated, going back to the structure of the object
passed to lmFit

On Tue, May 10, 2011 at 5:30 AM, Alberto Goldoni
<alberto.goldoni1975 at gmail.com> wrote:
> Dear All,
> i'm analyzing agilent microarrays with the "rgug4130a.db" database and
> using the function:"topTable(fit2,number=500,adjust="BH")" i have
> obtained 500 genes like these:
>
> Row     Col     ProbeUID        ControlType     ProbeName       GeneName        SystematicName  Description     X.hda.str...ref.        X.ref.str...ref.        X.hda.str...ref.str.    AveExpr F       P.Value adj.P.Val
> 16096   79      38      15309   0       A_43_P10328     CB606456        CB606456        unknown
> function        3.988290607     -0.951656306    4.939946913     10.29735936     36.77263264     0.000212298     0.641094595
> 8109    40      109     7609    0       A_42_P552092    203358_Rn       203358_Rn       Rat c-fos
> mRNA.   5.670956889     4.413365374        1.257591514     13.47699544     33.20342601     0.000292278     0.641094595
>
> but as you can see most genes like the first one  - CB606456 -  in the
> DESCRPTION there is written "unknown function".
>
> So i have performed a very simply search.
> 1) First in ENSAMBLE using the GeneName "CB606456" with the "Locations
> of DnaAlignFeature" it gives to me the Genomic location(strand): chr
> 7:16261621-16262210
> 2) Then in the Rat Genome Database
> (http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=735058) i have found
> that in this position there is one gene:
>
> 735058  GENE    Angptl4 angiopoietin-like 4     7       16261623        16267852
>
> so the question is why in the "rgug4130a.db" database the R system
> gives to me "unknown function" when using the genomic location in
> ensamble and then in rgd it gives to me the Angptl4 gene!
>
> and there is a function in order to do to R to perform this kind of
> search automatically? (this why in my 500 genes there are 100 "unknow
> function" genes and it will be interesting to have a function that
> perform this kind of search automatically).
>
>
> Best regards to all and to whom answer to me.
>
> --
> -----------------------------------------------------
> Dr. Alberto Goldoni
> Parma, Italy
>
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