When using ChAS, is it important for someone to back up their data?
Out of the six data files mentioned in the preceding question, it is important to backup and archive the ARR, CEL, CYCHP, and CHPCAR files at a minimum. This will allow someone to maintain the ability to either reanalyze from the CEL file or re-visualize the results using the CYCHP/CHPCAR files.
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What data files are produced during assay and analysis process when using ChAS?
A total of six files are produced that are key to the process:
ARR file: this file includes sample information.
AUDIT file: this file is a log of the sample history.
DAT file: this file is the raw data from the scanner.
CEL file: this file is the gridded and processed data.
CYCHP file: this file is the output of ChAS and contains all of the analysis data.
CHPCAR file: this file stores user-annotated calls, interpretations, and modifications made to CHP file segment data (ChAS 2.0 and higher).
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What is the mosaic call determination in ChAS?
The algorithm is designed to detect only mosaicism between ~30-70% for CNs between 1 and 3 for regions on the order of 5,000 markers in size or larger. The endpoint location of mosaic segments is less precise than the CN segmentation, with endpoint variation within 500 markers being typical for segments of 5,000 markers or larger. Some regions of full integer CN 1 or 3 below 5,000 markers in length may be incorrectly called as mosaic segments.
Some regions of CN below 1 or above 3, mosaic or otherwise, less than 5,000 markers in length may be incorrectly called as mosaic segments.
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What is the library file location for ChAS?
The library file location for ChAS 2.1 and above is C:\Affymetrix\ChAS\Library.
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How do I unzip the array library file if I have to install it manually?
Right click the zip folder and click extract all. They can also use an already installed software that unzips files (e.g., Winzip, 7-zip, or any other equivalent software). Browse to the location to save the folder and click Extract. Go to the folder to find the files.
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