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I want to load data related to a microarray gene expression experiment into caArray. Where should each piece of data go in caArray?
Answer
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A microarray gene expression experiment is typically associated with the following types of files: array design files, sample annotation files, and raw and/or processed data files. In addition, a user might also want to associate with a particular experiment, files that describe the experiment, files that describe the samples, and other miscellaneous files.
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In this step, slightly different processes are used to load data into caArray for different array platforms.
- Step #Step 3A : Import data under the MAGE-TAB format
- #Step 3B Import experimental data using the Affymetrix platform
- Import experimental data using the Illumina platform
- Import experimental data using the Genepix platform
- Import experimental data using the Agilent platform
- Import experimental data using the ImaGene platform
- Import experimental data using the Nimblegen platform one
- #Answer
Step 3A
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Import data under the MAGE-TAB format
Only file types listed in the flow diagram below can be imported.
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According to the figure above, to import a MAGE-TAB file, first select the Data tab on the Experiment Details page, then proceed to upload and validate the file you wish to import. The following MAGE-TAB file formats can be both imported and parsed by caArray: SDRF and IDF, along with their associated data files (Affymetrix CEL and CHP). MAGE-TAB data matrix file formats can be imported, but not parsed.
Step 3B
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Import experimental data using the Affymetrix platform
Because of a known issue concerning importing Affymetrix DAT files, uploaded Affymetrix DAT files should be kept in the "Manage Data" tab under the "Data" tab for a selected experiment for caArray versions up to version 2.1.1. Once the issue is resolved, Affymetrix DAT files will be able to be imported the same way as EXP, RPT, and TXT files.
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