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Question: Should I use the Annotations tab or MAGE-TAB annotation Files to annotate my experiment?
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Topic: caArray Usage
Date entered: 02/12/2009
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Release: Up to
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caArray 2.2
Question: Annotation Tab vs. MAGE-TAB Annotation Files in caArray
Answer:
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Date entered: 02/12/2009
Answer
caArray offers two options to annotate the experiment.
- You can annotate the experiment
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- automatically (recommended) by uploading/Importing MAGE-TAB formatted annotation files
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- (caArray 007 - MAGE-TAB Files).
- You can annotate the experiment manually by entering data using the Annotations tab, as described in the caArray User's Guide.
This knowledge base entry aims to clarify the difference and
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help you
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find an efficient way to annotate your experiment.
Differences between
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Annotations Tab and MAGE-TAB annotation files
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The
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Annotations 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
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, as shown in the illustration. Detailed
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definitions and explanations for each subtab can be found in the Annotations tabs section, of the caArray User's Guide
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.
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.
Subtabs of the Annotation Tab
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A MAGE-TAB file is a simple tab-delimited, spreadsheet-based file. IDF and SDRF are the related MAGE-TAB
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annotation files.
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The table below compares
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using Annotation Tab and MAGE-TAB annotation files.
Task | Annotations Tab | MAGE-TAB File |
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Entering Annotation Annotations Data | Click on "Annotation Tab" to annotation user interfacethe Annotations Tab in caArray. Enter annotation annotations field by field. | Upload pre-created Tabtab-delimited Data MAGE-TAB files (IDF & and SDRF filesformat). Annotation data need needs to be validated and imported together with the array data files referred referenced in SDRF filesfile(s). |
Modifying Annotation Data | Flexible. Your unpublished annotation data can be modified on the annotation user interface in caArray | Flexible with some limitations. Biomaterial related characteristics/attributes can be modified or added via annotation user interface. |
Auto Generated Annotation | During data import, caArray offers options of associating array data with the existing annotations or auto-creating new annotations for a Source - Sample - Extract - Labeled Extract - Hybridization chain based on the data imported. You may can enter the rest of the annotations on the annotation interface after the auto reactionchain has been created. | The Annotation information in IDF & and SDRF files will be is 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 Annotations cannot be downloaded. Only the data file associated with annotation annotations can be downloaded. | Annotation files can be downloaded. However, the annotation annotations added or modified via the Annotation interface will not be downloaded. |
Re-usability | Vocabulary entered can be reused by the other experiments. But annotation need to , but the annotations must 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
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In summary, the annotation user interface (
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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
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are visible but un-editable on caArray. Furthermore, MAGE-TAB files are portable and reusable,
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thus saving time and effort, especially when a large set of samples are collected from the same source.
Read For more information about about MAGE-TAB related files Click Here
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, refer to caArray 007 - MAGE-TAB Files.
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