Chapter 15. Array LIMS

Table of Contents

15.1. Array designs
15.1.1. Properties
15.1.2. Importing features to an array design
15.2. Array batches
15.3. Array slides
15.3.1. Creating array slides
15.3.2. Multiple slides wizard

Arrays are at the core of the BASE business and are essential elements to describe in order to be MIAME compliant. It is also critical to track and manage information about microarray design as accurately as possible since mistakes could prove extremely costly in downstream analysis. As a good practice, all array related information should be entered into BASE prior to work on describing the sample processing and hybridizations or other events making up an experiment is begun.

15.1. Array designs

Array designs should be understood as a plan which can be realized during a printing process producing microarray slides. During the course of the printing process, reagents may run out leading to the interruption of this process. All slides created during this printing process belong to the same printing batch. It is the array slide that will eventually be used in a hybridization event. BASE allows user to track those 3 entities with great details. This is an important functionality for users producing their own arrays and for those caring for quality control and tracking of microarray slides in a printing facility. The following sections detail how to use BASE to help in these tasks.

[Note] Non-array platforms also need array designs

Array designs are needed also for non-array platforms (eg. sequencing). In this case a "virtual array design" is created which is simply a list of all features that is of interest in the experiment. Since there are no coordinates or positions to identify features a unique id need to be constructed in some other way. For example, in sequencing experiments we may use a GTF file to create a virtual array design using the transcript_id and chromosome as a unique identifier.

Use Array LIMSArray designs to get to the list page with array designs.

15.1.1. Properties

Figure 15.1. Array design properties

Array design properties

Name

Provide an sensible name for the design (required).

Platform

Select the platform / variant used for the array design. The selected options affects which files that can be selected on the Data files tab.

Arrays/slide

The number of sub-arrays that can be placed on a single slide. The default value is 1, but some platforms, for example Illumina, has slides with 6 or 8 arrays. In sequencing platforms, this value is the number of lanes on a flow cell.

Description

Provide other useful information about the array design in this text area.

Click on the Save button to store the information in BASE or on the Cancel button to abort.

The Data files tab allows BASE users to attach files to the array design. The possible file types are defined by the array design's platform. See Section 11.4, “Selecting files for an item” for more information.

The Annotations tab allows BASE users to use annotation types to refine array design description. More about annotating items can be read in Section 10.2, “Annotating items”.

This Inherited annotations tab contains a list of those annotations that are inherited from the array design's parents (eg. plates). Information about working with inherited annotations can be found in Section 10.2.1, “Inheriting annotations from other items”.

15.1.2. Importing features to an array design

Importing features is an important step in order to fully define an array design. It should be noted that BASE does not enforce the immediate feature import upon creation of array design. However, it is STRONGLY advised to do so when creating an array design. Performing the import enables use of the array design in downstream analysis with no further trouble. It also matters when importing raw bioassay data and matching those to the corresponding array design.

Depending on which platform and/or data files you selected when you created the array design the process to import features is different. For example, if you selected the Affymetrix platform, which is a file-only platform, the feature information has already been extracted from the CDF file (if you selected one). If the selected platform doesn't extract information from the selected data file automatically this may be done manually by executing an import plug-in.

From the array design item view, click on the Import button and use the reporter map importer and an appropriate plug-in configuration when following the instructions in Chapter 18, Import of data. If the import run is successful, go to the array design list view. The Has features column will show Yes (db: x, file: y) where x is the number of features actually imported into the database.

[Note] Note

The Import button only shows up if the logged in user has enough permissions.

[Note] Verify that probsets in a CDF file exist as reporters

File-only platforms, such as Affymetrix, require that all probesets must exist as reporters before data can be analysed. For other platforms this is usually checked when importing the features to the database. Since no import takes place for file-only platforms, another manual step takes it place. Use the Import button in the array design item view and select the Affymetrix CDF probeset importer plug-in. If you have enough permissions this function will also let you create missing reporters.

15.2. Array batches

Beside the common way of creating items in BASE, an array batch can also be created directly from an array design, both in list view and single item view.

In list view of array design

Click on the icon available from the Batches column of the array design you want to use.

[Tip] Tip

As default in BASE the Batches column is hidden and need therefore be made visible first, see Section 5.4.3, “Configuring which columns to show”

New batch… is the corresponding button in single item view. The current array design will automatically be filled in the array design property for the new batch.

Figure 15.2. Array batch properties

Array batch properties

Name

The name of the array batch (required).

Array design

Array design that is used for the batch.

Print robot

The print robot that is used.

Protocol

The printing protocol that was followed when producing the array batch

Description

Provide other useful information about the array batch in this text area.

Click on the Save button to store the information in BASE or on the Cancel button to abort.

15.3. Array slides

Use Array LIMSArray slides to get to the list page of array slides.

15.3.1. Creating array slides

In BASE, array slides can be created, except the common way, by 2 routes:

from the array batch list page

Clicking on the icon in the Slides column for the batch you want to add a slide to. Corresponding button in the view page of a batch is New slide… .

using a wizard to create multiple slides simultaneously

This can be started from three different places:

  • array batch list view by clicking on in the Slides column of the batch that should be used.

  • Using the Create slides in a single item view of an array batch.

  • In the list page of array slides, using the Create multiple… button

The wizard is described further down in Section 15.3.2, “Multiple slides wizard”.

Figure 15.3. Create new array slide

Create new array slide

Name

The name of the array slide (required).

Barcode

Does the array slide have a barcode, it can be put here.

Destroyed

This check-box can be ticked to mark the slide as destroyed, lost or damaged.

Array batch

Array batch that the slide belongs to (required).

Index

The index of the array slide in selected array batch.

Description

Any information useful information about the slide can be in this field.

Click on the Save button to store the information in BASE or on the Cancel button to abort.

15.3.2. Multiple slides wizard

As mentioned above there is an alternative to create one slide at a time if you have many to add. There is a wizard that can help you to create at the most 999 slides in one go. The wizard is in two steps:

Figure 15.4. Create multiple array slides - step 1

Create multiple array slides - step 1

The first step reminds alot of the normal edit window of an array slide:

Name

The name prefix of the array slides. Each array slide will be numbered according to the start at and pad size settings below.

Array batch

Array batch that the slides belongs to (required).

Quantity

Number of slides to create with this wizard (required and must be between 1 and 999)

Start at

The index number to start from when indexing the name of the slides.

Pad size

The index will be filled out with zeros in front to always have this length.

Click on Next to move on to the second step of the wizard.

Figure 15.5. Create multiple array slides - step 2

Create multiple array slides - step 2

This step allows the names of the array slides to be adjusted if needed. It is also possible to enter barcodes for each of the new slides. The information can either be filled in one-by-one or by using the "scratchpad" icon . This opens up a larger text window where the names or barcodes can be entered one per line. This can be useful if the information can be pasted from an external source.

Click on the Save button to store the information in BASE or on the Cancel button to abort the wizard.