Changes between Version 19 and Version 20 of se.lu.onk.IlluminaSNPNormalization


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Timestamp:
Jun 9, 2008, 3:37:04 PM (13 years ago)
Author:
markus
Comment:

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  • se.lu.onk.IlluminaSNPNormalization

    v19 v20  
    6767  }}}
    6868
    69   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.
     69  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 and can be used as alternatives for ''--beadchip''. 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.
    7070   
    7171
    7272''Other information''
    7373
    74 CNV probes are not normalized by tQN; for these probes the original X and Y intensities from !BeadStudio are kept. tQN may result in a slightly  smaller number of SNPs having data. The reason for this reduction is that some SNPs have not been genotyped in the !HapMap samples used to generate the cluster files.
     74CNV probes are not normalized by tQN; for these probes the original X and Y intensities from !BeadStudio are kept. tQN may result in a slightly  smaller number of SNPs having data. The reason for this reduction is that some SNPs have not been genotyped in the !HapMap samples used to generate the cluster files. Cluster files for additional beadchip types can be generated upon request.
    7575
    7676=== Contact ===