[BioC] Error message when working with sam

[Holger Schwender]

Hi Jim, hi Assa,

thanks for drawing my attention to this bug. In the next few weeks, I will add some functionality to the functions which automatically set the arguments to FALSE if the corresponding mapping does not exist in the annotation package. But I am not sure if this will happen before the next release of BioConductor.

Best,
Holger


-------- Original-Nachricht --------
> Datum: Thu, 26 Mar 2009 08:30:07 -0400
> Von: "James W. MacDonald" <jmacdon at med.umich.edu>
> An: Assa Yeroslaviz <frymor at gmail.com>
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] Error message when working with sam

> Hi Assa,
> 
> Assa Yeroslaviz wrote:
> > Hi,
> > 
> > I'm trying to link my sig. genes with the web. by doing so I tried both
> > sam2html and link.siggenes:
> > 
> > sam2html(samresult, 20, "samresults_overview.html",
> chipname="ath1121501")
> > 
> > link.siggenes(samresult, 20, filename="samresults.html", addDataFrame =
> > TRUE, title="SAM results - stress",
> >         entrez = FALSE, refseq = FALSE, symbol = TRUE, omim = FALSE, ug
> =
> > FALSE,
> >         fullname = TRUE, which.refseq = "NM", chipname="ath1121501",
> > cdfname="ath1121501")
> > 
> > I keep getting the error messagees:
> > Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
> >   variable "ath1121501ENTREZID" was not found
> 
> That's because there are no mappings between this chip and Entrez Gene 
> IDs in the ath11215001.db package. You can see what mappings do exist by 
> loading the package and then using the ls() function:
> 
>  > library(ath1121501.db)
> Loading required package: AnnotationDbi
> Loading required package: DBI
>  > ls(2)
>   [1] "ath1121501"             "ath1121501_dbconn" 
> "ath1121501_dbfile"
>   [4] "ath1121501_dbInfo"      "ath1121501_dbschema" 
> "ath1121501ACCNUM"
>   [7] "ath1121501ARACYC"       "ath1121501ARACYCENZYME" "ath1121501CHR" 
> 
> [10] "ath1121501CHRLENGTHS"   "ath1121501CHRLOC" 
> "ath1121501CHRLOCEND"
> [13] "ath1121501ENZYME"       "ath1121501ENZYME2PROBE" 
> "ath1121501GENENAME"
> [16] "ath1121501GO"           "ath1121501GO2ALLPROBES" 
> "ath1121501GO2PROBE"
> [19] "ath1121501MAPCOUNTS"    "ath1121501ORGANISM"     "ath1121501PATH" 
> 
> [22] "ath1121501PATH2PROBE"   "ath1121501PMID" 
> "ath1121501PMID2PROBE"
> [25] "ath1121501SYMBOL"
> 
> 
> If you look at the help for the functions you are trying to use, you 
> will see that there is an 'entrez' argument that you can set to FALSE so 
> it won't try to do Entrez Gene mappings. Depending on what mappings do 
> exist in this annotation package, you may need to set other arguments to 
> FALSE as well.
> 
> Best,
> 
> Jim
> 
> 
> > 
> > Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
> > ifnotfound = NA) :
> >   error in evaluating the argument 'envir' in selecting a method for
> > function 'mget'
> > 
> > so I was forced toturn them off. Is there a way of using this
> information.
> > I'm using R2.8.1 with Bioconductior 2.3. (I think)
> > 
> > THX,
> > 
> > Assa
> > 
> > 	[[alternative HTML version deleted]]
> > 
> > _______________________________________________
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> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
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> 
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