caArray Usage
Date entered: 02/12/2009
Release Up to: caArray 2.2
Question: Annotation Tab vs. MAGE-TAB Annotation Files in caArray
Answer:
caArray offers two options to annotate the experiment: uploading/Importing MAGE-TAB formatted annotation files or manually entering data via the annotation user interface (Annotation Tab), see caArray User Guide P. 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 (see figure below). Detailed definations and explanations for each subtab can be found in caArray User Guide(P.34).
MAGE-TAB file is a simple tab-delimited, spreadsheet-based file. IDF and SDRF are the related MAGE-TAB's annotation files. Table below compares the differences between using Annotation Tab and MAGE-TAB annotation files.
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 & 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 Your unpublished annotation data can be modified on annotation user interface |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. |
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 annotation 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 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.
Read more about MAGE-TAB related files Click Here
Have a comment? Please leave your comment in caArray End User Forum
