[BioC] Error using yeastPkgBuilder (AnnBuilder package)

[Marc Carlson]

melany black wrote:
> Hi,
>    
>   I'm trying to build an annotation package for yeast chips using AnnBuilder.
>   I was successful, but at the end, I got an error.
>   Here's my code:
>    
>   > library("AnnBuilder")
>   
>> read.table(file.path(.path.package("AnnBuilder"), "data", "yeastsgd"),sep = "\t", header = FALSE, as.is = TRUE)[1:5,]
>>     
>           V1         V2
> 1 A_75_00001 S000005688
> 2 A_75_00002 S000005689
> 3 A_75_00003 S000005690
> 4 A_75_00004 S000005691
> 5 A_75_00005 S000005692
>   
>   
>> myBase <- file.path(.path.package("AnnBuilder"), "data", "yeastsgd")
>> myDir <- tempdir()
>> yeastPkgBuilder(pkgName="yeastAgilent",pkgPath=myDir,base=myBase,version = "1.1.0",
>>     
> +                 author = list(authors = "mel", maintainer ="mel.black at yahoo.fr"), fromWeb=TRUE)
>   
> package directory structure initialized
> annotation data read complete
> 1:1 PROBE mappings complete
> 1:many PROBE mappings complete
> CHRLOC complete
> Error in l2e(dList, env) : require a list
> Warning messages:
> 1: Organism Saccharomyces cerevisiae is not supported by GoldenPath (GP). in: getUCSCUrl(organism) 
> 2: no argument for max ; -Inf is returned in: max(i) 
>    
>   The following files were created in "yeastAgilent\data" folder:
>   yeastAgilentALIAS.rda
>   yeastAgilentCHR.rda
>   yeastAgilentCHRLOC.rda
>   yeastAgilentDESCRIPTION.rda
>   yeastAgilentGENENAME.rda
>   yeastAgilentORF.rda
>   yeastAgilentPMID.rda
>    
>   Hope someone could explain me where this error comes from, and how to fix it.
>    
>   > sessionInfo()
> R version 2.5.1 (2007-06-27) 
> i386-pc-mingw32 
>   locale:
> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
>   attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
>   other attached packages:
>         GO AnnBuilder   annotate        XML    Biobase 
>   "1.16.0"   "1.14.0"   "1.14.1"    "1.9-0"   "1.14.1" 
>    
>    
>   Mel.
>
>        
> ---------------------------------
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>   
Hi Melany,

After some testing I have discovered that the major source of your
problem is that you are not using the correct kind of IDs. 
YeastPkgBuilder is older code and was apparently designed before SGD IDs
saw wider usage.  You will have better luck if you first convert to
"ORF" style IDs.  So in your case the 1st 5 rows of your base file
should look more like:

A_75_00001      YOR162C
A_75_00002      YOR163W
A_75_00003      YOR164C
A_75_00004      YOR165W
A_75_00005      YOR166C

Instead of:

A_75_00001    S000005688
A_75_00002    S000005689
A_75_00003    S000005690
A_75_00004    S000005691
A_75_00005    S000005692

Please rest assured that we are working towards getting rid of these
kinds of problems in the future.


     Marc