[BioC] Error message when working with sam

[Holger Schwender]

Hi Assa,

I have finally fixed this bug and committed the improved version (1.19.2) to BioConductor. It is available in the devel section:

http://bioconductor.org/packages/2.5/bioc/html/siggenes.html

Sorry that this took so long, but I have just moved and changed my job. So fixing the bug took much longer than normal.

I have tested if sam2html works now correctly. And it seems to work. But I only have data for which all the annotations exist. So I would be grateful if you could apply sam2html to your data again and tell me if it works (it should give you some warnings about, e.g., that ENTREZID is not available, and return a html-file without the missing annotation).

Thanks a lot,
Holger 





############################################
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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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
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> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> 
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