How to create a custom probe filter

When you apply a filter to a list of probes from a probe search, the filter removes the probes that do not satisfy the criteria defined in the filter. You can create as many custom probe filters as you like based on your own criteria. Filters are application-specific, so if you create a filter for one application, it is not available in any another.

Note: Probe filters are not available for microRNA or SureSelect Capture Array type probes. Also, you cannot apply a custom probe filter to the results of an HD or SNP probe search.

Click the Workspace tab (or enter a collaboration).
Set the application type.
Click My Account > User Preferences.

The User Preferences page appears.
In Select Preference Type, select Manage filters, then click Submit.

A search results pane appears, with a list of existing filters (if any) for your account.
Click Create Filter.

The Create Filter page opens in a new window.
Define the following attributes of the new custom probe filter. All are required.

Attribute	Instructions/Details
Filter Name	Type a unique name for the filter. This name appears in the list of available probe filters.
Filter Description	Type a brief description of the filter. This information appears next to your filter in the description column of the list of available filters.
Filter Option	Select one of the following filter options: Select the best <n> probes for each <annotation type> — Type the desired number of probes in the box, and select an annotation type from the list. Your custom filter will return up to that number of best probes that are associated with each different value of your selected annotation type, that meet the criteria defined in the filter. Example: If you type 25 for best <n> probes, and select Accession as the annotation type, the filter returns the 25 best probes associated with each accession that meet your filter criteria. If there are fewer than 25 probes associated with the accession, the filter returns all probes associated with that accession that meet the criteria. Select All Probes — Your custom filter returns all of the probes that meet your filter criteria.
Variable Name	Select the desired probe variable from the drop-down list. Probe variables are the attributes of probes that eArray evaluates during the probe filtering process. Examples: The Length variable represents the number of nucleotides in a probe, and the is_validated variable defines whether or not a probe has been empirically validated by Agilent, using microarray experiments. The selection you make here influences the choices available to you in the Operator drop-down list. Also, the variables available differ by application type.
Operator	Select the desired operator from the drop-down list. The selected operator defines the way eArray evaluates probe variables. Example: If you select the is greatest operator for the Length variable, the filter returns the probe(s) with the greatest length. Some operators require a cut-off value, which you specify in Value.
Value	Type a cut-off value, without units. If this field is unavailable, no cut-off value is needed. Example: To create a filter that returns only probes that are longer than 40 nucleotides, select Length as the Variable Name, greater than as the operator, and type 40 in Value.

Click Save.

eArray saves your custom filter and makes it available for you to use in eArray. Its name and description appear in the Search Results pane of the User Preferences page.

You can select the filter (or another one in the list) as your default filter. In the Actions column of the Search Results pane, next to the desired filter, click Set Default. When you produce a list of probes with a probe search, you simply click Apply Default Filter to apply the default filter to the probe list.