[BioC] AnnBuilder: ABPkgBuilder gives missing GO and NAs in ACCNUM

Thu Jul 5 16:15:06 CEST 2007

Dear list.

I have ran into trouble when creating an annotation for 89 genes. 
Although I do not get any errors I have the following trouble:
1) the GO-environments are missing
2) the GenBank-environment (i.e. ACCNUM) are NAs.

Any insight as to why I have this problem is greatly appreciated. Thanks 
for the help/advice in advance.

Below are the codes and output I got when I ran the ABPkgBuilder.

Regards,
chuen seng

#############################
#My file with identifiers (which are entrez IDs) looks like this, it is 
tab-separated:
id1    92
id2    23394

#############################
#This is my code:
mysrcUrls<-getSrcUrl("all","Homo sapiens")
ABPkgBuilder(baseName="data/baseName.txt", srcUrls=mysrcUrls,
                  baseMapType="ll",pkgName="chip89",
                  pkgPath="C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation",
                  organism="Homo sapiens", version="1.1.0",
                  author=list(author="Chuen Seng",maintainer 
="chuenseng.tan at ki.se"),
                  fromWeb = TRUE)

#############################
#These are some of the output I get when I ran the code above:

Attaching package: 'GO'

        The following object(s) are masked from package:AnnBuilder :

         GO

Scalar value @vals[2] better written as $vals[2] at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl3b8efd3.pl line 19.
Use of uninitialized value in exists at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl3b8efd3.pl line 33, 
<DATA> line 1.
Scalar value @vals[2] better written as $vals[2] at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerld073f66.pl line 19.
Use of uninitialized value in exists at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerld073f66.pl line 33, 
<DATA> line 1.
Scalar value @vals[2] better written as $vals[2] at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl3d991f9b.pl line 19.
Use of uninitialized value in exists at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl3d991f9b.pl line 37, 
<DATA> line 1.
Scalar value @vals[2] better written as $vals[2] at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl2e2d6b25.pl line 19.
Use of uninitialized value in string ne at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl2e2d6b25.pl line 33, 
<DATA> line 1.
Use of uninitialized value in split at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl2e2d6b25.pl line 34, 
<DATA> line 1.
Use of uninitialized value in string ne at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl2e2d6b25.pl line 37, 
<DATA> line 1.
Use of uninitialized value in string ne at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl2e2d6b25.pl line 37, 
<DATA> line 1.
Use of uninitialized value in exists at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl2e2d6b25.pl line 47, 
<DATA> line 1.
Scalar value @vals[2] better written as $vals[2] at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl490a41f6.pl line 19.
Scalar value @vals[2] better written as $vals[2] at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl5f3c4bea.pl line 19.
Use of uninitialized value in exists at 
C:\DOCUME~1\cmetcs\LOCALS~1\Temp\RtmpYLygsb\tempPerl5f3c4bea.pl line 33, 
<DATA> line 1.
Read 1 item
Read 1 item
[1] "4000 2 2"
The following data sets have been added to the database and will be removed:
 [1] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89ACCNUM.rda"      

 [2] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89CHR.rda"         

 [3] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89CHRLENGTHS.rda"  

 [4] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89CHRLOC.rda"      

 [5] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89ENTREZID.rda"    

 [6] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89ENZYME.rda"      

 [7] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89ENZYME2PROBE.rda"
 [8] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89GENENAME.rda"    

 [9] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89MAP.rda"         

[10] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89MAPCOUNTS.rda"   

[11] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89OMIM.rda"        

[12] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89ORGANISM.rda"    

[13] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89PATH.rda"        

[14] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89PATH2PROBE.rda"  

[15] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89PFAM.rda"        

[16] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89PMID.rda"        

[17] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89PMID2PROBE.rda"  

[18] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89PROSITE.rda"     

[19] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89QC.rda"          

[20] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89QCDATA.rda"      

[21] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89REFSEQ.rda"      

[22] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89SYMBOL.rda"      

[23] "C:/Documents and 
Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/data/chip89UNIGENE.rda" 

#############################
#These are some of the output I get when loaded the annotation package I 
did:
 > library(chip89)
 > chip89()

Quality control information for  chip89
Date built: Created: Thu Jul 05 21:38:39 2007 

Number of probes: 89
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
         chip89ACCNUM found 0 of 89
         chip89CHR found 89 of 89
         chip89CHRLOC found 89 of 89
         chip89ENTREZID found 89 of 89
         chip89ENZYME found 24 of 89
         chip89GENENAME found 89 of 89
         chip89MAP found 89 of 89
         chip89OMIM found 87 of 89
         chip89PATH found 64 of 89
         chip89PMID found 89 of 89
         chip89REFSEQ found 89 of 89
         chip89SYMBOL found 89 of 89
         chip89UNIGENE found 89 of 89
Mappings found for non-probe based rda files:
         chip89CHRLENGTHS found 25
         chip89ENZYME2PROBE found 15
         chip89ORGANISM found 1
         chip89PATH2PROBE found 67
         chip89PFAM found 84
         chip89PMID2PROBE found 11526
         chip89PROSITE found 75

#############################
#These are the info from sessionInfo()
 > sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.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"   "1.14.0"