The Experiment List view allows you to import and manage the data within your ArrayStar project. The Experiment List appears automatically when you select File > New Project, and also after building a project with the Project Setup Wizard. The Experiment List can also be accessed by selecting Data > Show Experiment List.
The Experiment List view is composed of several elements. Text-based displays in the left-hand panel are discussed in this topic. The toolbar tools at the top of the left-hand panel, and the Info Pane on the right are described in separate topics.
Shortcut links in the Experiment List:
Near the top left of the Experiment List are shortcut links to relevant dialogs and wizards. The links available depend on the experiment type and on whether the project was just created or not.
|
Hyperlink text |
Shortcut to… |
|
Do you have experiment attributes to import? |
Import Experiment Attributes tool ( |
|
Do you need to create/edit custom experiment attributes? |
Create/Edit User Defined Experiment Attributes
tool ( |
|
Do you need to create replicate sets? |
Create New Replicate Set tool ( |
|
Would you like to begin filtering to find gene sets of interest? |
The Quick Gene Set Creation dialog |
|
Would you like to see a scatter plot? |
Graphs > Scatter Plot command and the Open
Scatter Plot View tool ( |
Creating new categories:
Categories are groupings of experiments and appear as folders on the left side of the Experiment List view. Categories are the highest level of organization for your data within ArrayStar.
When you initially import data into your project, it is usually placed in the “Imported” folder (see image above). However, if you imported a SeqMan NGen assembly, the experiments may be grouped, by default, into separate folders based on workflow.
The following example shows the Experiment List for an RNA-Seq assembly in which variants were also calculated. One folder contains the RNA-Seq expression information for each experiment, while the other contains SNP data. This grouping allows for distinct gene-level comparisons based on different types of analysis of the same assembly:
To create a new category, click the Create New
Category tool 
. The following
are examples of possible categories: Wildtype/Mutation, European/African/Asian,
or Control/Disease. Any categories you set up will be accessible via a drop-down
menu in the Advanced Filtering
dialog. You can change the name of a category by selecting the item and then
clicking the Rename/Edit Selected Item tool 
.
Creating replicate sets:
Replicate sets are the next level of organization after
categories. To create a new replicate set, click the Create New
Replicate Set tool 
.
ArrayStar lets you create two levels of replicate sets. The top level represents
biological replicates. The second level (a replicate set created within a
replicate set) represents technical replicates. Organize your experiments by
dragging and dropping them onto the replicate sets you have created.
Right-click shortcuts in the Experiment List:
Right-click in the main (left) section of the Experiment List view to access shortcuts to items in the Experiment List Toolbar:
|
Right-click location |
Context menu option |
Shortcut to… |
|
Anywhere |
Import experiment attributes |
Import Experiment Attributes tool ( |
|
Open scatter plot view |
Graphs > Scatter Plot command and the Open
Scatter Plot View tool ( | |
|
On one or more files or folders |
Export experiment |
File > Export Selected Experiment command and
the Export tool ( |
|
Create new replicate set |
Create New Replicate Set tool ( | |
|
Rename/edit |
Rename/Edit tool ( | |
|
Delete |
Delete tool ( |
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