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


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Timestamp:
Jun 9, 2008, 12:04:33 PM (13 years ago)
Author:
markus
Comment:

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  • se.lu.onk.IlluminaSNPNormalization

    v7 v8  
    1818
    1919''Requirements''
    20   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.
     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).
    2121
    2222''Input data format''
     
    5050  }}}
    5151
    52   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.
     52  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.
    5353   
    5454