Page History

Problem: A caArray experiment captures as much relevant information about a real-world experiment as possible. This can include general information about the experiment, such as the experimental design and experimental factors, associated publications, protocols, array designs, quality control and data processing steps, or specific information about biological materials used in the experiment.

Topic: caArray Usage

Release: caArray 2.0 and above

Date entered: 10/12/2011

Solution: Files containing data generated for an experiment can be uploaded, validated and imported into a caArray experiment. Once a user clicks on an experiment at the caArray web interface, five main menu items are presented for each experiment: Overview, Contacts, Annotations, Data, and Publications.

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• • Hybridizations: This page captures information related to hybridizations on microarray chips. It establishes linkage between data files collected after hybridization and the corresponding labeled abstracts from which the data are derived. In most cases the hybridization information comes from the loading of a MAGE-TAB SDRF

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    file.
• Data: This collection of pages provides access to data loading, processing, and downloading.
  • Data loading and processing: Data are first loaded into the "Manage Data" tab, typically using the MAGE-TAB format. Once they are processed (validated and imported, or classified as supplemental files), they are automatically removed from the "Manage Data" tab and moved to the "Imported Data" tab or the "Supplemental Files" tab.
  • Data download: A user can download the whole dataset or any subset of data here. This page offers three download options:
    • Download Experiment File Packages: it allows download of pre-packaged files.
    • Download Selected Experiment Files: it allows download of a selected set of files.
    • Export Experiment Annotation Packages: it allows the export of experiment annotation in either MAGE-TAB or GEO SOFT (some restrictions apply) format.
• Publications: This page lists all publications added by the experiment owner. The information on this page either comes from manual data entry or comes from the loading of a MAGE-TAB IDF file.

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