[BioC] AnnBuilder questions

[John Zhang]

>
>I tried to check the library, everything worked well
>except the following error :
>
>Problem number 1 :
>
>'yeastAgilentLOCUSID' is deprecated
>rather use 'yeastAgilentENTREZID'
>see help("Deprecated")

This applies to packages containing an Entrez gene id environment (named 
XXXENTREZID now but used to XXXLOCUSID). Since the yeast annotation pacakge does 
not have Entrez Gene id, you may just ignor the warning. 



>
>In fact help("Deprecated") didn't help me at all!
>
>
>Here's what my package looks like :
>
>> library("yeastAgilent")
>> yeastAgilent()
>
>
>Quality control information for  yeastAgilent 
>Date built: Created: Tue Aug 21 18:50:18 2007  
> 
>Number of probes: 41419 
>Probe number missmatch: yeastAgilentALIAS;
>yeastAgilentCHR; yeastAgilentCHRLOC;
>yeastAgilentDESCRIPTION; yeastAgilentENZYME;
>yeastAgilentGENENAME; yeastAgilentGO; yeastAgilentORF;
>yeastAgilentPATH; yeastAgilentPMID 
>Probe missmatch: None 
>Mappings found for probe based rda files: 
>         yeastAgilentALIAS found 1800 of 41419
>         yeastAgilentCHR found 5653 of 41419
>         yeastAgilentCHRLOC found 4968 of 41419
>         yeastAgilentDESCRIPTION found 5653 of 41419
>         yeastAgilentENZYME found 814 of 41419
>         yeastAgilentGENENAME found 4634 of 41419
>         yeastAgilentGO found 5653 of 41419
>         yeastAgilentORF found 6934 of 41419
>         yeastAgilentPATH found 1190 of 41419
>         yeastAgilentPMID found 5560 of 41419 
>Mappings found for non-probe based rda files:
>         yeastAgilentCHRLENGTHS found 17
>         yeastAgilentENZYME2PROBE found 475
>         yeastAgilentGO2ALLPROBES found 4404
>         yeastAgilentGO2PROBE found 2991
>         yeastAgilentORGANISM found 1
>         yeastAgilentPATH2PROBE found 99
>         yeastAgilentPMID2PROBE found 42190 
>
>
>- Problem number 2 : the number of probe should be
>41418 and not 41419 (I checked my base file, it has
>41418 lines)
>
>- Problem number 3 : very few probes have been
>annotated (1800 out of 41419 I guess)
>for example if I do:
>>getinf=function(g,flds=c("ALIAS","CHR","CHRLOC")){
>>  sapply(flds,function(x) lookUp(g, "yeastAgilent",
>x))
>>  }  
>> getinf("A_75_P0006546")
>$ALIAS.A_75_P0006546
>[1] NA
>
>$CHR.A_75_P0006546
>[1] NA
>
>$CHRLOC.A_75_P0006546
>[1] NA
>
>I just get a bunch of "NA"s, except for a very few
>number of probes.
>
>- Problem number 4 : YeastPkgBuilder doesn't create
>"yeastAgilentSYMBOL". It seems like this is always the
>case with this function.
>How can I overcome this? Because if I want to plot my
>probes on the chromosome using geneplotter, I get an
>error:
>
>> library("geneplotter")
>> chrLoc=buildChromLocation("yeastAgilent")
>Error in get(x, envir, mode, inherits) :
>"yeastAgilentSYMBOL" not found
>That's a real problem, because quite all the purpose
>of creating an annotation package was for using
>geneplotter. 
>
>Here's my sessionInfo:
>
>> 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_Fr
ance.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
>
>attached base packages:
>[1] "tools"     "stats"     "graphics"  "grDevices"
>"utils"     "datasets"  "methods"   "base"     
>
>other attached packages:
>       YEAST           GO   AnnBuilder          XML   
> hgu95av2  geneplotter      lattice     annotate     
>Biobase yeastAgilent 
>    "1.16.0"     "1.16.0"     "1.14.0"      "1.9-0"   
> "1.16.0"     "1.14.0"     "0.16-3"     "1.14.1"    
>"1.14.1"      "1.1.0" 
>
>
>Thanks for any comment.
>
>Mel.
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084