View statistics on your microarray using the Array Calculator

Array Calculator calculates the number of microarrays of a given format that are needed to accommodate a specified set of probes, as well as other statistics. It can also help you choose an appropriate design format for your microarrays. For a given design format, the number of open features that you can populate with probes can vary, due to differences in the applied control grids for different application types.

Set the application type.
In the Microarray tab in your individual user or collaboration workspace, or on a page of probe search results, click Array Calculator.

Array Calculator opens in a new window, which remains open as you navigate eArray. You can open multiple Array Calculator windows.

If you opened Array Calculator from a set of probe search results, the total number of probes in the search results appears in Number of Probes.
Set the following parameters. Both are required unless otherwise noted.

Parameter

Instructions/Details

Species

Select the desired species from the list.

This is mandatory for the CGH, ChIP, and microRNA application types. It is optional for the Expression application type, as there is only one (non-species specific) control grid per array format for this application type.

Probes

Select one of these options:

Number of Probes – Performs calculations based on a specified number of probes. If you select this option, enter the number of probes in the box.

Probe Groups – Performs calculations based on probe groups that you select.

To calculate based on probe groups, click Add. Otherwise skip to Step 6.

A probe group selection page opens in a new window. For details on how to use this page to select probe groups, see Select probe groups for probe searches.

You can add as many probe groups as you like. Be sure to include replicate and normalization probe groups, if appropriate.
Specify the following about each probe group.

Parameter

Instructions/Details

Control Type

Select one of these options:

biological – Designates that the probe group is not a control (condition = FALSE). It is the default choice for biological probes, which should comprise at least 50% of your design.
pos – Designates the probe group as a positive user control. Although positive controls are excluded from many of the statistical QC metrics in Feature Extraction, they are available for downstream analysis. Positive controls generally have predictable signals, but this is not a requirement. An example of positive controls present on the Agilent control grid is the Agilent spike-in probes, which are used in the gene expression application for calculating QC metrics following addition of spike-in controls to the sample.
ignore – Omits the probe group from Feature Extraction analyses and output. Once an array design is submitted, the Control Types cannot be changed, so the only way to "re-activate" them, if desired, is to modify the ControlType field of the design file.
neg – Designates the probe group as a negative user control. Negative control groups are intended to have no hybridization. The control grid that is assigned automatically to each design contains an adequate number of negative controls. If you assign your own additional group of negative controls, these negative controls are used by Feature Extraction for background determination (whether or not they have only background signal).

The control type of a probe group influences both the position and the number of copies of its probes in microarray sets. For a more detailed discussion, see Edit microarray designs/sets.

Replicate

(Not available for positive or negative control probe groups) Type the number of copies of each probe group to include in the calculation.

In Design Format, select the desired configuration. Design formats contain a fixed number of features that can be populated by probes. For example, the 4 x 44K design format contains four identical replicate arrays on one slide, and each array contains approximately 44,000 features. To have Array Calculator select an appropriate design format and control grid for you, click Pick for me.

In Control Grid, a control grid appropriate for your chosen design format and application type appears. To see details about it in a new window, click the name of the control grid.

Control grids are specific for application type and, in some instances, species. For a given design format, there may be other control grids available. To select a different control grid, if one is available, follow these steps:

1. Next to the name of the current control grid, click .
  A list of applicable control grids appears in a new window.
2. Select the desired control grid, then click Done.
  The new control grid appears in Control Grid in the Array Calculator window.

A design format, with its associated control grid, has a set number of features that can be populated by user-defined probes.

Click Calculate.

Array Calculator calculates array statistics and displays them on the right side of the window. The table below describes these statistics.

Calculated Array Statistics

In Array Calculator, you can view calculated statistics about the set of microarrays that is needed to implement a particular microarray design. These calculated values also appear as you create microarray designs using wizards, and when you edit microarray designs. The available statistics vary by application type and by location within eArray.

Statistic	Description
Number of Microarrays per Slide	Number of replicate arrays that appear on each glass microarray slide. All of the arrays on the slide are identical. For example, the 4 x 44K array format places four identical replicate arrays on each slide.
Number of Slides	Total number of separate microarray slides needed to implement your microarray design. For formats containing multiple identical arrays on one slide, each of the arrays on the slide counts as one array. For example, if you type 65,000 as the number of probes, and select the 4 X 44K design format, Array Calculator returns 2 as the Number of Slides.
Total Number of Features	Number of features occupied by target probes and control probes, as well as all unused locations. For formats containing multiple identical arrays on one slide, this number reflects the total number of features in each array on the slide.
Number of Available Features	Number of “empty” unused locations in all microarrays. For formats containing multiple identical arrays on one slide, this number reflects the total number of available features in each array on the slide.
Number of Agilent Controls	Number of features occupied by standard Agilent control probes. For formats that contain multiple replicate arrays on one slide, this number reflects the number of Agilent control probes in each array on the slide.
Number of User Controls	Number of features occupied by control probes specified by the user. For formats that contain multiple identical arrays on one slide, this number reflects the number of user control probes in each array on the slide.
Percentage Filled	Percentage of features occupied collectively by biological probes and control probes
Percentage filled using fill array	Percentage of features occupied collectively by all biological and control probe groups, including Agilent control probe groups and the probe group that you may have selected to fill unused features.
Number of Features Occupied by SNP Probes	SNP probes are specifically designed for CGH+SNP microarrays, which include both CGH probes and SNP probes on the same array.
Number of microRNA Targets Covered	(microRNA application type only) Total number of microRNA targets associated with probes on the array.
Number of Distinct microRNA Targets Covered	(microRNA application type only) Total number of microRNA targets associated with probes on the array, excluding microRNAs with duplicate sequences. For example, for a multi-species array, if two microRNAs have the same sequence, this value considers them together as a single microRNA. eArray treats microRNAs that have the same sequence as a single species of microRNA, and lays out only one set of probes for it. This avoids the problem of two sets of probes competing for the same target material. The competition would otherwise compromise the specificity of the assay.
Number of Distinct microRNA targets that can be covered by remaining space	(microRNA application type only) Number of microRNAs that you can still select for the array, without exceeding its capacity. Note: eArray treats microRNAs that have the same sequence as a single species of microRNA, and lays out only one set of probes for it.