Changes between Version 27 and Version 28 of se.lu.onk.IlluminaSNPNormalization

Timestamp:

Sep 16, 2008, 11:07:21 AM (16 years ago)

Author:

markus

Comment:

--

se.lu.onk.IlluminaSNPNormalization

@@ -61 +61 @@
   }}}
 
-  This command will perform tQN on the samples in the tQN subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform tQN on a subset of samples you can edit ''sample_names.txt'' accordingly. The normalized data is stored in the tQN subdirectory ''normalized''. For each sample, there is a file with tQN normalized data. A file ''tQN_beadstudio.txt'' is also generated with tQN BAF and Log R Ratios for all samples in a format suitable for import into !BeadStudio using its import sub-column process. tQN also supports generating tQN data for further analysis with PennCNV and QuantiSNP. Running tQN with the following command:
+  This command will perform tQN on the samples in the tQN subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform tQN on a subset of samples you can edit ''sample_names.txt'' accordingly. The normalized data is stored in the tQN subdirectory ''normalized''. For each sample, there is a file with tQN normalized data. A file ''tQN_beadstudio.txt'' is also generated with tQN B allele frequencies and Log R ratios for all samples in a format suitable for import into !BeadStudio using its import sub-column process. tQN also supports generating tQN data for further analysis with PennCNV and QuantiSNP. Running tQN with the following command:
 
   {{{  
@@ -70 +70 @@
    
 
-''Other information''
+''tQN B allele frequencies and log R ratios''
 
-  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. tQN cluster files for additional beadchip types can be generated upon request.
+  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. A detailed description of how tQN X and Y intensities are turned into tQN BAF and tQN log R ratios is available [http://cbbp.thep.lu.se/~markus/software/ReadMe_calculation_BAF_Log_R_Ratio.pdf?format=raw here]. 
+
+''Supported beadchip types''
+
+tQN cluster files for additional beadchip types can be generated upon request.
 
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