[BioC] AnnBuilder questions

[melany black]

Dear all,

I tried to build an annotation package using
AnnBuilder and YeastPkgBuilder function. 
I think I'm close to the end now, but I steel have
some errors I don't really understand...

Here's the code I used:

> library("AnnBuilder")
> read.table(file.path(.path.package("AnnBuilder"),
"data", "sgdid"),sep = "\t", header = FALSE, as.is =
TRUE)[1:5,]
             V1        V2
1 A_75_P0000001    TEL01L
2 A_75_P0000002 YAL067W-A
3 A_75_P0000003   YAL067C
4 A_75_P0000004   YAL067C
5 A_75_P0000005   YAL067C
> myBase <- file.path(.path.package("AnnBuilder"),
"data", "sgdid")
>myDir <- tempdir()
>yeastPkgBuilder(pkgName="yeastAgilent",pkgPath=myDir,base=myBase,version
= "1.1.0",author = list(authors = "Mel", maintainer
="Mel <melany.black at yahoo.fr>"),fromWeb=TRUE)

I got the final annotation package, install it to R
using:

rcmd build yeastAgilent
rcmd build --binary yeastAgilent  

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")

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_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:
       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.