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 menu
option of the node (Figure 1).
Figure 1
Once the copy number and LOH analysis has been completed the data is stored in the node. Right mouse clicking on this node displays a menu containing the 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 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