The Set Up Attributes Dialog

The Set Up Attributes dialog allows you to create replicate sets based on:

• Available attributes for the loaded data

• Part of the chip or sample name

The dialog has several names and versions, depending on the type of experiment and the way in which the dialog is accessed. However, the contents of each version are nearly identical.

Experiment type	Dialog access	Dialog name	Description
Copy number variation (CNV), RNA-Seq, ChIP-Seq, miRNA or microarray	By creating a project in the ArrayStar Project Wizard	Set Up Attributes and Replicates	Allows you to create “replicate sets”. Replicate sets are used, for example, when the same experiment has been done multiple times and you want to use statistics to determine a single signal intensity value for each gene.
	After creating a project, from the Experiment List view by clicking on the Regroup replicates by name or attribute tool ()	Create Replicate Groups
Variants	By creating a project in the ArrayStar Project Wizard	Set Up Attributes and Categories	Allows you to create “categories” for Variants experiments based on any attribute of importance to you. The attributes from a Variants project can be used to group samples in different ways for filtering and statistical analysis (e.g. disease vs. normal).
Variants	After creating a project, from the Experiment List view by clicking on the Regroup categories by name or attribute tool ().	Create Category Groups

The following image shows an example of the dialog for a Variant project, accessed via the Project Setup wizard, and with the Show advanced options button checked.

ArrayStar evaluates all available attributes for the loaded chips/samples and displays the ones that are suitable for grouping as columns in the displayed table. The Experiment column lists the chips/samples that have been loaded.

If you wish to see all attributes, uncheck the box next to Show only grouping attributes. To group your experiments by a listed attribute, click the column header of that attribute.

If ArrayStar is unable to locate attributes for the loaded data, you may click on the Import Experiment Attributes button to browse to the attribute file you wish to import.

To enable editing or to map attributes to a project, check Force Custom Importing before clicking on the Import Experiment Attributes button. This launches the attribute file within the Custom Attribute Import Wizard, where you may edit it. Other than its name, this wizard is identical to the Data Import Wizard.

The bottom of the Set Up Attributes and Replicates dialog lets you choose how you wish to handle the creation of replicate sets. By default, only basic options are displayed. To see advanced options, some of which appear in the bullet points below, check Show advanced options at the top right of the dialog.

• To rename experiments using a listed attribute, select Rename experiments from an attribute and make a selection from the drop-down menu.

• To rename experiments using a regular expression, select Rename using regex pattern and type in the pattern.

• To create multiple replicate sets or categories, select Create replicate sets (or groups) from an attribute and make a selection from the drop-down menu. The selected attribute column in the table will display the proposed replicate sets in alternating colors.

• To automatically create groups using part of the chip/sample name, select Create groups using a selection in the name. Highlight a portion of the chip/sample name in the adjacent box. An additional column, labeled Group, will be added to the table, showing the proposed replicate sets based on the grouping you specified. The proposed replicate sets or categories will be shown in alternating colors.

• To automatically create groups using a regular expression that is part of the file name, select Create groups using regex pattern on the name and type in the pattern.

Click Next to process your data and proceed to the next step of the wizard; Cancel to close the Project Setup Wizard without adding any data to the project; or Back to return to the Add Experiments to Import step of the Project Setup Wizard.

Note: Clicking Back will not allow you to return to the Preprocessing dialog to get a different normalization. Once normalization has been done, that dialog is unavailable unless the experiment itself is changed.