Question: AnnBuilder: ABPkgBuilder gives missing GO and NAs in ACCNUM
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gravatar for Chuen Seng, Tan
12.2 years ago by
Chuen Seng, Tan10 wrote:
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/dat a/chip89ACCNUM.rda" [2] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89CHR.rda" [3] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89CHRLENGTHS.rda" [4] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89CHRLOC.rda" [5] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89ENTREZID.rda" [6] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89ENZYME.rda" [7] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89ENZYME2PROBE.rda" [8] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89GENENAME.rda" [9] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89MAP.rda" [10] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89MAPCOUNTS.rda" [11] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89OMIM.rda" [12] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89ORGANISM.rda" [13] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89PATH.rda" [14] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89PATH2PROBE.rda" [15] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89PFAM.rda" [16] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89PMID.rda" [17] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89PMID2PROBE.rda" [18] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89PROSITE.rda" [19] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89QC.rda" [20] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89QCDATA.rda" [21] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89REFSEQ.rda" [22] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/chip89SYMBOL.rda" [23] "C:/Documents and Settings/cmetcs/Desktop/data/cellminer/both/data/annotation/chip89/dat a/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"
ADD COMMENTlink modified 12.2 years ago by Marc Carlson7.2k • written 12.2 years ago by Chuen Seng, Tan10
Answer: AnnBuilder: ABPkgBuilder gives missing GO and NAs in ACCNUM
0
gravatar for Marc Carlson
12.2 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Chuen, You should not get Genbank ID's from LocusLink ID's since there is no way to know which reported Genbank sequence would match to the ID. If all you have is a LocusLink ID then all you have is a gene based identifier and the Genbank information has therefore been "lost". Nianhua is correct that you should not get a lot of PERL spam like that. Just from looking at your post, this really looks to me like your PCs/environment is causing issues for you. I will send you a personal email in a second to request your ID file to see if I can make it work here. Thanks, Marc
ADD COMMENTlink written 12.2 years ago by Marc Carlson7.2k
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