Changes between Version 8 and Version 9 of se.lu.onk.IlluminaSNPNormalization


Ignore:
Timestamp:
Jun 9, 2008, 2:20:33 PM (13 years ago)
Author:
markus
Comment:

--

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  • se.lu.onk.IlluminaSNPNormalization

    v8 v9  
    2020  tQN is written in R with a Perl wrapper, so both R and Perl are required. Required Perl modules are: File::Spec, Getopt::Long, IO::File and Pod::Usage (http://www.cpan.org). Required R package is limma (http://www.bioconductor.org).
    2121
     22''Installation''
     23  Download and unzip the file available under the section ''Download tQN'' on this page.
     24
     25  OS X or Linux:
     26  The programs should run as they are. You need R and perl in your path.
     27
     28  Windows:
     29  Depending on how you have installed R and Perl on your system you may have to edit the variable ''$R_command'' at the beginning of the file ''tQN_normalize_samples.pl'' so it contains the full path to your R executable. For example, we have successfully used tQN using !ActivePerl on a Window system with the following ''$R_command'':
     30  {{{
     31  # Mac OS X and Linux
     32  # my $R_command="R --vanilla --no-save --slave < tQN.R";
     33  # Windows
     34  my $R_windows=File::Spec->canonpath('C:/"Program Files"/R/R-2.7.0/bin/Rscript');
     35  my $R_command="$R_windows --vanilla tQN.R";
     36  }}}
     37 
     38
    2239''Input data format''
    2340  tQN is applied to data exported from !BeadStudio. For a set of samples, the file exported from !BeadStudio should be tab-delimited in the following format:
     
    3047
    3148  {{{ 
    32   ./split_beadstudio_samples.pl --beadstudio_file=example/example_beadstudio_data.txt
     49    split_beadstudio_samples.pl --beadstudio_file=example/example_beadstudio_data.txt
    3350  }}}
    3451  where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above.
     
    4158
    4259  {{{ 
    43    ./tQN_normalize_samples.pl --beadchip=humancnv370-duo
     60     tQN_normalize_samples.pl --beadchip=humancnv370-duo
    4461  }}}
    4562
     
    4764
    4865  {{{ 
    49    ./tQN_normalize_samples.pl --beadchip=humancnv370-duo --output_format=PennCNV
     66     tQN_normalize_samples.pl --beadchip=humancnv370-duo --output_format=PennCNV
    5067  }}}
    5168