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

Timestamp:

Jun 9, 2008, 2:20:33 PM (16 years ago)

Author:

markus

Comment:

--

se.lu.onk.IlluminaSNPNormalization

@@ -20 +20 @@
   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).
 
+''Installation''
+  Download and unzip the file available under the section ''Download tQN'' on this page.
+
+  OS X or Linux:
+  The programs should run as they are. You need R and perl in your path.
+
+  Windows:
+  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'':
+  {{{
+  # Mac OS X and Linux
+  # my $R_command="R --vanilla --no-save --slave < tQN.R";
+  # Windows
+  my $R_windows=File::Spec->canonpath('C:/"Program Files"/R/R-2.7.0/bin/Rscript');
+  my $R_command="$R_windows --vanilla tQN.R";
+  }}}
+  
+
 ''Input data format''
   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:
@@ -30 +47 @@
 
   {{{  
-  ./split_beadstudio_samples.pl --beadstudio_file=example/example_beadstudio_data.txt
+    split_beadstudio_samples.pl --beadstudio_file=example/example_beadstudio_data.txt
   }}}
   where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above.
@@ -41 +58 @@
 
   {{{  
-   ./tQN_normalize_samples.pl --beadchip=humancnv370-duo
+     tQN_normalize_samples.pl --beadchip=humancnv370-duo
   }}}
 
@@ -47 +64 @@
 
   {{{  
-   ./tQN_normalize_samples.pl --beadchip=humancnv370-duo --output_format=PennCNV
+     tQN_normalize_samples.pl --beadchip=humancnv370-duo --output_format=PennCNV
   }}}