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Filter By Flags


The Filter By Flags command will filter variables and observation based on any number of flags that are stored within your data. You can filter based on one or more flags, and use AND/OR operation on these flags, group your flags by covariates, apply ALL/ANY logic on each group, and filter either variables or observations. A new "List" is generated from this command, and can be used with all further analysis (as well as for use with the Filter tab of the View Controller).

Input Data Requirements

It works on -Omic data types.

To run this module, type MicroArray | Preprocess | Filter by Flag.

Filter Flag menu.png

General Options



  • Project & Data: The window includes a dropdown box to select the Project and Data object to be filtered.
  • Variables: Selections can be made on which variables should be included in the filtering (options include All variables, Selected variables, Visible variables, and Customized variables (select any pre-generated Lists)).
  • Observations: Selections can be made on which observations should be included in the filtering (options include All observations, Selected observations, Visible observations, and Customized observations (select any pre-generated Lists).
  • Output name: The user can choose to name the output data object.


  • The user can choose to either Filter variables or Filter observations.
  • The Group by drop-down box can be used to choose a column (either from the Design Table for filtering variables or the Annotation Table for filtering observations) to group the filtering criteria. For instance, if the experiment contains a Time and Treatment column, the user may be interested in using this column as a group by which to filter.
  • The If all groups meet the criterion radio box, when selected, will allow a variable (or observation) to pass the filter criteria only if ALL groups meet the criteria, while the If any group meets the criterion radio box will allow a variable (or observation) to pass the filter criteria if ANY group meets the criteria.


The Flags section is used to add the individual flag criteria.

  • Enable intensity filter with cutoff - Allows the user to filter the data based on a particular intensity value cutoff.
  • A logical operator drop down box allows the user to add multiple flags using the AND/OR operators.
  • The Group count drop down box includes the comparison operator (>=, =, <=, etc...), and a value field to specify the number of items in the group that must meet the specified criteria.

Output Results

Clicking submit will run the Filter and create a new List in the Solution Explorer. This List can then be used to filter variables in further analyses.

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