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Creation of input data.

The data is created using Affymetrix's genotyping console to analyse the CEL files from a SNP 6.0 microarray chip. While it is possible to obtain data from the SNP 5.0 microarray chips, the file format of the exported data files is significantly different from the SNP 6.0 data file format and so cannot be read by CNViewer. The creation and export of the data requires a number of sets in the Genotyping Console which may take a significant amount of time to complete. The first step is to perform the copy number/LOH analysis by clicking on the Perform the Copy Number/LOH analysis... menu option of the Itensity Data node (Figure 1).

Figure 1

Figure 1

Once the copy number and LOH analysis has been completed the data is stored in the Copy Number/LOH Results node. Right mouse clicking on this node displays a menu containing the Export Number/LOH Results... menu option. After selecting this option a number of windows are displayed allowing the selection of which files to export data from and then which parameters to export (Figure 2).

Figure 2

Figure 21

CNViewer does not require all the different parameters to be export and doing so will create very large text files (Figure 3). Due to their size and the number of data points it is impractical to manually view the files as either a text document or a spread sheet document.

Figure 3

Figure 3



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