Creation of input data.
Affymetrix's genotyping console is used to analyse the CEL files from a SNP 6.0 microarray chip and export the CNV data to text files. 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
When the copy number and LOH analysis has finished, 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 the files to export data from and then which parameters to export (Figure 2).
Figure 2
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
Last modified 5th July 2011