Once you have created a probe list using the filtering tool you can open up a basic probe list view. To do this simply double-click on a probe list in the data view.
The probe list viewer shows the probe name and genomic position. It also shows the data column which was added by the filter which created it. In some cases this column is blank, but often it contains useful information (eg p-values).
If you double click on any line in the probe list view then the main display will update to show you the region of the genome which contains that probe.
Under the Reports menu there is an option to create an annotated probe list. This is an expanded version of the probe list which tries to map your probes to features in your genome and can optionally export ratio data.
Since there is no direct mapping of probes to features you need to choose what type of feature you want to try to map to, and the positional relationships you are looking for between your probes and the feature.
If you want to export ratio data then you can do this from within the annotated probe report. The report will contain the data for every Data Store which is currently visible in your chromosome view.
As with the probe list you can double click on any line in the annotated probe list to show that probe in the main display.
The other reporting option is the probe group report. The options for this are similar to the annotated probe list except that you get an extra option which allows you to specify a distance within which you will group probes together so that you get a single entry on the report which covers multiple probes.
For the annotation of probe groups you have two extra options. You can choose to annotate with all features completely contained within the area of the group, or with all features which overlap with the group. All the other options available for the probe list report are still present and if these are selected then each probe is annotated individually, and the results are combined in the final report.
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