Changes between Version 7 and Version 8 of se.lu.onk.IlluminaSNPNormalization

Timestamp:

Jun 9, 2008, 12:04:33 PM (16 years ago)

Author:

markus

Comment:

--

se.lu.onk.IlluminaSNPNormalization

@@ -18 +18 @@
 
 ''Requirements''
-  tQN is written in R with a Perl wrapper. Required Perl modules are: File::Spec, Getopt::Long, IO::File and Pod::Usage. Required R package is limma.
+  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).
 
 ''Input data format''
@@ -50 +50 @@
   }}}
 
-  generates one data file per sample in the tQN subdirectory ''normalized'' for further analysis using PennCNV. Alternatives for ''--output_format'' are ''QuantiSNP'', which generates one data file per sample for further analysis with QuantiSNP and ''!BeadStudio'', which is the default argument generating the default ''tQN_beadstudio.txt'' file with data for all samples. Beadchip types for which there is a cluster file in the tQN subdirectory ''lib'' are supported by tQN.
+  generates one data file per sample in the tQN subdirectory ''normalized'' for further analysis using PennCNV. Alternatives for ''--output_format'' are ''QuantiSNP'', which generates one data file per sample for further analysis with QuantiSNP and ''!BeadStudio'', which is the default argument generating the default ''tQN_beadstudio.txt'' file with data for all samples. Beadchip types for which there is a cluster file in the tQN subdirectory ''lib'' are supported by tQN. For PennCNV and QuantiSNP, SNPs having missing values in either B allele frequencies or log R ratios after normalization are excluded from the respective output files.