
Dear Bioconductor List.

I got some nice suggestions before, but Im still having problems.
I cannot be network settings since Ive tried on different locations  
using different networks. And I tried it with R 2.5.0 using the same  
versions of packages as Nianhua Li but it still didnt work. So my  
guess is that some files that ABPkgBuilder is using for annotation  
has changed?

Basically, Ive tried to annotate our in-house human oligo chip using  
three different starting points. Genbank, Refseq and Gene. I manually  
downloaded the files and parsed them to get from genBank to gene. If  
I start using Refseq or Genbank the ABPkgBuilder executes as normal  
and creates a package that can be built and installed but all the  
information for the probes contain NA. If I instead use Gene I get it  
all to work. So, it seem to work as long as the ABPkgBuilder doesnt  
have to do the parsing to GeneID:s. But in this case you loose the  
probe information about which sequence (genBank ID:s) has been used.  
So any suggestions? I supply my code below.

Best regards
// Johan Lindberg

########################
#if installing the package built using genbank ID:s
library(hsOligo)
ls("package:hsOligo")
blockList <- contents(hsOligoGENENAME, all.names)
test <- unlist(blockList[])
test[1:10]
HUMv321F10 HUMv321F11 HUMv321F12 HUMv321F13 HUMv321F14 HUMv321F15  
HUMv321F16 HUMv321F17
         NA         NA         NA         NA         NA          
NA         NA         NA
HUMv321F18 HUMv321F19
         NA         NA

########################
########################
#if installing the package build using gene ID:s
library(hsOligo)
ls("package:hsOligo")
blockList <- contents(hsOligoGENENAME, all.names)
test <- unlist(blockList[])
test[1:10]
test[1:10]
                                  
HUMv321F10                                 HUMv321F11
       "SUMO1/sentrin specific peptidase 6"                         
"CDC-like kinase 4"
                                  
HUMv321F12                                 HUMv321F13
"interphotoreceptor matrix proteoglycan 1"                         
"CDC-like kinase 4"
                                  
HUMv321F14                                 HUMv321F15
     "vascular endothelial growth factor A"                     
"protocadherin beta 15"
                                  
HUMv321F16                                 HUMv321F17
     "vascular endothelial growth factor A"    "hepatitis A virus  
cellular receptor 1"
                                  
HUMv321F18                                 HUMv321F19
                                          
NA                                         NA
###########################################
#HOW I DID MY ANNOTATION

#HUM-OLIGO
library(Biobase)
library("annotate")
library("AnnBuilder")
#The appearance of my baseName-file with genBank
HUMv301D01      AF160499
HUMv301H01      BC006454
HUMv301L01      AB011130
HUMv301P01      AL031259
HUMv301D13      AC005539
.
.
#Genbank
AnnWd <- "C:/Annb/humOligoV3.0.2.txt"
AnnWd2 <- "C:/Annb/humOligo/gb"
mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens")
ABPkgBuilder(baseName=AnnWd, srcUrls=mySrcUrls, baseMapType =  
"gb",pkgName="hsOligo", pkgPath=AnnWd2, organism = "Homo sapiens",  
version = "1.1.1", author = list(author = "Johan Lindberg",  
maintainer = "johanl@biotech.kth.se"), fromWeb = TRUE)
#The appearance of my baseName-file with Refseq
HUMv301D01      NM_009589
HUMv301H01      NM_005890
HUMv301L01      NM_006030
HUMv301P01      NM_002793
HUMv301D13      NM_173355
.
.
#Refseq
AnnWd <- "C:/Annb/humOligoRefseq.txt"
AnnWd2 <- "C:/Annb/humOligo/refseq"
mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens")
ABPkgBuilder(baseName=AnnWd, srcUrls=mySrcUrls, baseMapType =  
"refseq",pkgName="hsOligo", pkgPath=AnnWd2, organism = "Homo  
sapiens", version = "1.1.1", author = list(author = "Johan Lindberg",  
maintainer = "johanl@biotech.kth.se"), fromWeb = TRUE)

#The appearance of my baseName-file with Gene
HUMv301D01      414
HUMv301H01      NA
HUMv301L01      9254
HUMv301P01      5689
HUMv301D13      151531
.
.
#Gene
AnnWd <- "C:/Annb/humOligoGene.txt"
AnnWd2 <- "C:/Annb/humOligo/gene"
mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens")
ABPkgBuilder(baseName=AnnWd, srcUrls=mySrcUrls, baseMapType =  
"ll",pkgName="hsOligo", pkgPath=AnnWd2, organism = "Homo sapiens",  
version = "1.1.1", author = list(author = "Johan Lindberg",  
maintainer = "johanl@biotech.kth.se"), fromWeb = TRUE)

###########################################

sessionInfo()

R version 2.4.1 (2006-12-18)
i386-apple-darwin8.8.1
locale:
C
attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"      
"datasets"  "methods"
[8] "base"
other attached packages:
Biobase  hsOligo
"1.12.2"  "1.1.1"
###########################################
###########################################
###########################################
###########################################



On Feb 21, 2007, at 3:16 AM, Nianhua Li wrote:
Hi Johan,

I created a package by using your script and the probe-GenBank mapping
(5 lines)showed in your email. It looks fine:

Quality control information for  Hum30kbatch1to5
Date built: Created: Tue Feb 20 17:43:09 2007

Number of probes: 5
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
          Hum30kbatch1to5ACCNUM found 5 of 5
          Hum30kbatch1to5CHRLOC found 4 of 5
          Hum30kbatch1to5CHR found 4 of 5
          Hum30kbatch1to5ENTREZID found 4 of 5
          Hum30kbatch1to5ENZYME found 2 of 5
          Hum30kbatch1to5GENENAME found 4 of 5
          Hum30kbatch1to5GO found 4 of 5
          ...

I am using R 2.5 though (sessionInfo below). GO 1.51.1 and GO 1.14.1 are
the same. AnnBuilder 1.12.0  should work well on R 2.4. And your script
is fine. Maybe it is environment setting or network problem?

hope this is helpful

nianhua

sessionInfo()
R version 2.5.0 Under development (unstable) (2007-01-22 r40546)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;
LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;
LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"      
"datasets"
[7] "methods"   "base"

other attached packages:
         GO AnnBuilder   annotate        XML    Biobase
   "1.15.1"  "1.13.14"   "1.13.4"    "1.4-0"  "1.13.34"

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*********************************************
Johan Lindberg
Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
School of Molecular Biotechnology
Department of Gene Technology
Visiting address:
Roslagstullsbacken 21, Floor 3
106 91 Stockholm, Sweden
Delivering address:
Roslagstullsvägen 30B
104 06 Stockholm, Sweden
Phone (office) +46 8 553 783 44
Fax + 46 8 553 784 81
http://www.ktharray.se/
http://www.arrayadvice.se/
*********************************************




*********************************************
Johan Lindberg
Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
School of Molecular Biotechnology
Department of Gene Technology
Visiting address:
Roslagstullsbacken 21, Floor 3
106 91 Stockholm, Sweden
Delivering address:
Roslagstullsvägen 30B
104 06 Stockholm, Sweden
Phone (office) +46 8 553 783 44
Fax + 46 8 553 784 81
http://www.ktharray.se/
http://www.arrayadvice.se/
*********************************************



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