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Question: How do I use the Annotation Tab versus MAGE-TAB Annotation Files in caArray?

Contents

Topic: caArray Usage

Release: Up to caArray 2.2

Date entered: 02/12/2009

Answer

caArray offers two options to annotate the experiment: uploading/Importing MAGE-TAB formatted annotation files (caArray 007 - What are the MAGE-TAB Files?) or manually entering data via the annotation user interface (Annotation Tab). Refer to the caArray User Guide (page 34). This knowledge base entry aims to clarify the difference and helps you to find an efficient way to annotate your experiment.

Differences between Annotation Tab and MAGE-TAB annotation files

The Annotation tab opens with seven subtabs for entering annotation data for the experiment you are creating: Experimental Design, Experiment Factors, Source, Extracts, Labeled Extract and Hybridizations, as shown in the illustration. Detailed definitions and explanations for each subtab can be found in the caArray User Guide(page 34).

Subtabs of the Annotation Tab
Screenshot showing Subtabs of the Annotation Tab

A MAGE-TAB file (caArray 007 - What are the MAGE-TAB Files?) is a simple tab-delimited, spreadsheet-based file. IDF and SDRF are the related MAGE-TAB annotation files. The table below compares using Annotation Tab and MAGE-TAB annotation files.

Features

Annotation Tab

MAGE-TAB File

Entering Annotation Data

Click on "Annotation Tab" to annotation user interface. Enter annotation field by field.

Upload pre-created Tab-delimited Data files (IDF and SDRF files). Annotation data need to be validated and imported together with the array data files referred in SDRF files(s).

Modifying Annotation Data

Flexible. Your unpublished annotation data can be modified on annotation user interface

Flexible with some limitations. Biomaterial related characteristics/attributes can be modified or added via annotation user interface.
Experimental factor, protocol, design, or publication related attributes can not be changed. They become read-only after files are imported.
The additional annotation data added through annotation interface can not be downloaded (see below).

Auto Generated Annotation

During data import, caArray offers options of associating array data with the existing annotations or auto-creating new annotations for Source - Sample - Extract - Labeled Extract - Hybridization chain based on the data imported. You may enter the rest of annotations on the annotation interface after the auto reaction.

The Annotation information in IDF & SDRF files will be automatically assigned to each annotation field during the data import. If a biomaterial node is missing in the Source - Sample - Extract - Labeled Extract - Hybridization chain, appropriate intermediate nodes are automatically generated to complete the chain.

Portability

Annotation can not be downloaded. Only the data file associated with annotation can be downloaded.

Annotation files can be downloaded. However, the annotation added or modified via the Annotation interface will not be downloaded.

Re-usability

Vocabulary entered can be reused by the other experiments. But annotations need to be selected or entered in each new experiment.

Annotation files can be downloaded and reused for different experiments with the necessary modifications, such as the name of the data files.

Best Usage

Experiments with few sources or samples. Useful for the experiments which can be described with the generic annotation data in caArray.

Complex experiments with large set of data, or experiments with many specific characteristics.

Summary

In summary, the annotation user interface (annotation tab) offers a straight forward and quick way to enter annotation data. MAGE-TAB annotation files allow the user to create complex annotations and keep annotation editing and maintenance manageable at the same time. MAGE-TAB files allow users to enter the annotations that are not displayed as generically available and editable fields in the annotation user interface. These customized annotation data entered via MAGE-TAB files will be visible but un-editable on caArray. Furthermore, MAGE-TAB files are portable and reusable, which can save a lot of time or effort, especially when a large set of samples are collected from the same source.

For more information about about MAGE-TAB related files, refer to caArray 007 - What are the MAGE-TAB Files?.

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