[BioC] Annotation.db: how automatically call a mapping?

[Hooiveld, Guido]

Hi Martin,

Indeed, another useful, straigh-forward possibility for mapping. 
However, I am now facing the problem of properly combining the
annotation info with the expression data. This is what I would like to
do:

>Tab_data <- exprs(eset[probeids])
>Tab_data <- cbind(Tab_data, fit2$Amean) # to add average expression of
LIMMA output
>Tab_data <- cbind(Tab_data, fit2$p.value) # to add p-value of LIMMA
output
etc.

This al goes fine, however adding the annotation info 'mixes-up' the
content of Tab_data; the annotation data replaces the first column of
Tab_data, and the content of all cells is replaced by 'null'. I suspect
it has something to do with the type of object I would like to merge,
but I am not sure.

> map.entrez <- getAnnMap("ENTREZID", annotation(eset))
> map.entrez <- as.list(map.entrez[probeids])


> Tab_data <- cbind(Tab_data, map.entrez)
  ^ in R this seems to work, but when saved as .txt the content of
Tab_data is completely mixed up. Before 'adding' map.entrez Tab_dat is
OK.


> write.table(cbind(rownames(Tab_data2), Tab_data2),
file="test_1234.txt", sep="\t", col.names=TRUE, row.names=FALSE)

> class(Tab_data)
[1] "matrix"
> class(map.entrez)
[1] "list"
> 


Do you, or someone elsr, have a suggestion how to properly link these
two types of data?
Thanks again,
Guido



 

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Martin Morgan
> Sent: 30 June 2009 00:00
> To: Hooiveld, Guido
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Annotation.db: how automatically call a mapping?
> 
> Hooiveld, Guido wrote:
> > Hi,
> >  
> > I am facing a problem i cannot solve myselves, despite everything i 
> > read/know. But i assume the solution is easy for the more 
> knowledgable 
> > folks in BioC/R...
> >  
> > This does work:
> >> library(moe430a.db)
> >> xxyy <- moe430aSYMBOL
> >> xxyy
> > SYMBOL map for chip moe430a (object of class "AnnDbBimap")
> >  
> > However, for this to work you need to know the array type 
> of the data 
> > that is analyzed.
> >  
> >  
> > Now i would like to automatically extract the (e.g.) SYMBOL mapping 
> > from an annotation.db, thus by retrieving the array type 
> from the eset.
> >  
> >> library(affy)
> >> eset <- rma(data)
> >> probeids <- featureNames(eset)
> >> annotation(eset)
> > [1] "moe430a"
> >  
> > But how can i use this info to properly call the SYMBOL mapping?
> 
> Hi Guido --
> 
> to get the appropriate map
> 
>   library(annotate)
>   map = getAnnMap("SYMBOL", annotation(eset))
> 
> to select just the relevant probes
> 
>   map[probeids]
> 
> toTable(map[probeids]) or as.list(map[probeids]) might be the 
> next step in the work flow.
> 
> Martin
> 
> >  
> > I tried this:
> >> arraytype <- annotation(eset)
> >> arraytype <- paste(arraytype, "db", sep = ".") arraytype
> > [1] "moe430a.db"
> >> arraytype <- paste("package", arraytype, sep = ":") gh <- 
> >> ls(arraytype) gh
> >  [1] "moe430a"              "moe430a_dbconn"       "moe430a_dbfile"
> > "moe430a_dbInfo"       "moe430a_dbschema"     "moe430aACCNUM"
> > "moe430aALIAS2PROBE"   "moe430aCHR"           "moe430aCHRLENGTHS"
> > "moe430aCHRLOC"       
> > [11] "moe430aCHRLOCEND"     "moe430aENSEMBL"
> > "moe430aENSEMBL2PROBE" "moe430aENTREZID"      "moe430aENZYME"
> > "moe430aENZYME2PROBE"  "moe430aGENENAME"      "moe430aGO"
> > "moe430aGO2ALLPROBES"  "moe430aGO2PROBE"     
> > [21] "moe430aMAP"           "moe430aMAPCOUNTS"     "moe430aMGI"
> > "moe430aMGI2PROBE"     "moe430aORGANISM"      "moe430aPATH"
> > "moe430aPATH2PROBE"    "moe430aPFAM"          "moe430aPMID"
> > "moe430aPMID2PROBE"   
> > [31] "moe430aPROSITE"       "moe430aREFSEQ"        "moe430aSYMBOL"
> > "moe430aUNIGENE"       "moe430aUNIPROT"
> >  
> >> gh[33]
> > [1] "moe430aSYMBOL"
> >> symbols <- mget(probeids, gh[33])
> > Error in mget(probeids, gh[33]) : second argument must be an 
> > environment
> >  
> > This also doesn't work:
> >> symbols <- mget(probeids, envir=gh[33])
> > Error in mget(probeids, envir = gh[33]) : 
> >   second argument must be an environment
> >  
> > My approach thus is the wrong approach to automatically extract 
> > mappings from a annotation.db.
> > Since i don't know about any other possibility, i would 
> appreciate if 
> > someone could point me to a working solution.
> >  
> > Thanks,
> > Guido
> >  
> > 
> > ------------------------------------------------
> > Guido Hooiveld, PhD
> > Nutrition, Metabolism & Genomics Group Division of Human Nutrition 
> > Wageningen University Biotechnion, Bomenweg 2
> > NL-6703 HD Wageningen
> > the Netherlands
> > tel: (+)31 317 485788
> > fax: (+)31 317 483342 
> > internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
> > email:      guido.hooiveld at wur.nl 
> > 
> > 
> > 
> > 	[[alternative HTML version deleted]]
> > 
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