Hi again Nianhua.

To try the Perl-is-wrong hypothesis I tried to do the annotation on  
two different windows computers (which have worked using previous  
versions of AnnBuilder and R) here at the institution and both ended  
up with the same result. That is, the script executed as normal but  
all the annotation environments contain NA for all my identifiers.

Hmm, now Im really puzzled. Perhaps a certain version of Perl is  
required? Im currently having v5.8.6 installed on my MacBook.

Best regards

// Johan Lindberg

On Mar 6, 2007, at 9:55 AM, Johan Lindberg wrote:

> Thank you for your help Nianhua. Its greatly appreciated.
>
> I followed your instructions and everything went according to plan
> except for that the script didn't write anything to myoutput.txt (its
> empty). So I guess this is were the problem resides, but i have no
> idea what to do about it. Any suggestions?
>
> Best regards
>
> // Johan Lindberg
>
>
> On Mar 5, 2007, at 6:54 PM, Nianhua Li wrote:
>
>> Hi, Johan,
>>
>> Your perl configuration may have problem. The step of converting
>> GenBank accessions or RefSeq accessions to Entrez Gene ids is
>> performed by some perl scripts. The related functions are
>> "fileMuncher" and ".callperl" in the LL.R of AnnBuilder. Once
>> AnnBuilder gets the probe to Entrez Gene mapping, all other
>> annotations are retrieved by pure R functions. Therefore I guess your
>> perl may have problem. In your previous post, I observe this warning:
>>
>> perl: warning: Setting locale failed.
>> perl: warning: Please check that your locale settings:
>> 	LC_ALL = (unset),
>> 	LANG = "en_SE.UTF-8"
>>      are supported and installed on your system.
>>
>> And  your sessionInfo was:
>>> sessionInfo()
>> R version 2.4.1 (2006-12-18)
>> i386-apple-darwin8.8.1
>>
>> locale:
>> C
>>
>> This may be related to the problem. I am sure there are perl experts
>> on the list and they can provide very useful suggestions.
>>
>> To separate the perl problem from the AnnBuilder puzzle, please try
>> the following on your machine:
>>
>> 1. create a empty folder, say <tmp>
>> 2. copy your probe-to-GenBank mapping file
>> ("C:/Annb/humOligoV3.0.2.txt" ?) to <tmp> and rename to myinput.txt
>> 3. download ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz to
>> <tmp>, and unzip it to gene2accession.
>> 4. create an empty file named myoutput.txt
>> 5. copy AnnBuilder/scripts/egAccParser to <tmp> and rename to
>> egAccParser.pl
>> 6. add the following lines to the beginning of egAccParser.pl:
>> -----------------------------------------------------
>> #!/usr/bin/perl
>> open(BASE, "<myinput.txt") || die "Can not open myinput.txt";
>> open(DATA, "<gene2accession") || die "Can not open gene2accession";
>> open(OUT, ">myoutput.txt") || die "Can not open myoutput.txt";
>> ------------------------------------------------------
>> 7. from <tmp>, run: perl egAccParser.pl
>>
>> If everything works find, myoutput.txt should contain probe-to-Entrez
>> Gene mapping.
>>
>> hope this is helpful
>>
>> nianhua
>
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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/
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