[BioC] problem with rat database

[Alberto Goldoni]

@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")

> 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 at 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 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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>>
>



-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Parma, Italy