On Tue, May 10, 2011 at 8:17 AM, Alberto Goldoni <
alberto.goldoni1975@gmail.com> wrote:

> @Vincent
>
> The chip used is the "rgug4130a" so i have to use the "rgug4130a.db"
> database.
>
> In order to obtain the toptable this is my history:
>
> library(limma)
> library(vsn)
> targets <- readTargets("targets.txt")
> RG <- read.maimages(targets$FileName, source="agilent")
> MA <- normalizeBetweenArrays(RG, method="Aquantile")
> contrast.matrix <-
>
> cbind("(hda+str)-(ref)"=c(1,0),"(ref+str)-(ref)"=c(0,1),"(hda+str)-(ref+str)"=c(1,-1))
> rownames(contrast.matrix) <- colnames(design)
> fit <- lmFit(MA, design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
> geni500<-topTable(fit2,number=500,adjust="BH")
>
>
Hi, Alberto.

The data in your topTable result are taken from the feature extraction
result file.  In other words, rgug4130a.db is not used in what you show
above.  You could add to your annotation using either rgug4130a.db or
biomaRt, but you will need to perform these steps yourself.  As to why some
of your probes do not appear to have annotation, you would probably need to
contact Agilent as they are the source of your current annotation.

Hope that helps,
Sean


> > sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] AnnotationDbi_1.12.0 Biobase_2.10.0       limma_3.6.9
>
> loaded via a namespace (and not attached):
> [1] DBI_0.2-5     RSQLite_0.9-4 tools_2.12.1
>
>
>
> 2011/5/10 Vincent Carey <stvjc@channing.harvard.edu>:
> > 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@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@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
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
>
>
>
> --
> -----------------------------------------------------
> Dr. Alberto Goldoni
> Parma, Italy
>
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>

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