Question: What is the difference between the annotation options that are available when importing data?
Topic: caArray Usage
Release: caArray 2.X
Date entered: 06/30/2010
Details about the Question
We were manually uploading CHP and CEL files (as well as supplemental files) for 72 patients into our instance of caArray. When we were importing, caArray offered four annotation options. What is the difference between these options?
Answer
The import process is the last step of data uploading in caArray, which allows the array data to be stored in the database. During the importing process, caArray associates the data with the appropriate biomaterial and hybridization annotation by creating an annotation chain of source to sample to extract to labeled extract to hybridization. The array data can be downloaded only if the data were associated properly.
Import MAGE-TAB set
If a MAGE-TAB set (IDF and SDRF) is imported along with the data files, where the SDRF file refers to each of the data files, caArray will use the information provided in SDRF to determine how to create sources, samples, extracts, labeled extracts and hybridizations.
Import Only the datafile
If only data files (for example, .cel, .chp, etc.) are imported, caArray offers three options to associate the data and annotation.
Options to Associate the Data and Annotation
Option 1. Autocreate annotation sets ... for each selected file
For every unique file name to be imported, caArray automatically creates a Source - Sample - Extract - Labeled Extract - Hybridization chain corresponding to each data file imported.
Option 2. Autocreate a single annotation set ... for all selected files
caArray creates a single Source - Sample - Extract - Labeled Extract - Hybridization chain, and associates all selected data files with this single chain.
Option 3. Associate selected file(s) to existing biomaterial or hybridization
caArray displays all available sources, samples, extracts, labeled extracts and hybridizations. The user select one of these, and caArray associates the selected files with that biomaterial or hybridization. Note that additional items in the chain (to the right of the selected biomaterial) may need to be generated by the system.
Troubleshooting: Choose the right option
The proper association between the array data and annotation data is critical to a successful array data import.
The annotation data might be created before the data files were uploaded or imported. These annotation data, however, have to be used properly. For example, when the new biomaterial objects are created during the auto-create process, the biomaterial data manually entered would be ignored and associated with no datafiles.
If there are annotation data manually entered to the experiment prior to the importing process, the user should choose option 3 to select the hybridization object during the import so that there would be no downstream creation of biomaterial objects.
If user chooses one of the options of "Autocreate...", there should be no manual biomaterial annotation entered.
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