The Probe Group Report

The Probe Group Report is similar to the Annotated Probe Report except that it allows you to group together closely positioned probes to define larger regions of interest.

Options

• You can choose what sort of position a feature must have relative to a region of interest to become annotated. You can choose from overlapping, enclosed, closest, surrounding, upstream and downstream
• If you select anything other than overlapping or enclosed you need to set a cutoff for how far away a feature can be and still be associated with a region of interest.
• You can choose to omit any regions which couldn't be associated with a feature from the final report
• You can choose to append extra columns on the end of the report for all currently visible data stores which contain the average current quantitated data for each region
• You can choose how far apart adjacent probes can be to still be considered as part of the same region of interest. There is no limit to how many probes can be within a region of interest.

Output Columns

The columns in an annotated probe report are:

1. Chromosome
2. Start Position
3. End Position
4. Average Probe Value - When a filter creates a probe list it can associate a value with each probe in the list (p-value etc.). This column shows the average value for all probes in the region. Some filters don't add a value in which case this column will be blank.
5. Number of Probes - A count of how many probes were included in this region
6. Feature name - will be blank if there is no associated feature. For overlapping features there will be multiple entries in this column (and description) if the probe is overlapped by more than one feature
7. Description
8. Data Columns - if you selected to export data for current stores then there will be two extra columns per data store containing the mean and standard deviation of the set of current quantitated values for each set of probes

You can choose to sort the report on any of the columns. Just click on a column header to sort the data on that column. Click again to sort in the opposite direction.

If you double click on any line in the report the chromosome view will jump to that point in the genome so you can see the data underlying that region.

Saving the Report

If you press the Save button at the bottom you can save the full report to a file. The files created are tab-delimited text files which you should be able to open in a spreadsheet application for further processing. The saved report will keep the current order of the rows in the report.