Is there an equivalent metric for the "Offset Flag" in the QC and Sample Info tab in Chromosome Analysis Suite (ChAS) for OncoScan?
There is no available equivalent to the "Offset Flag" in the QC and Sample Info tab in ChAS. The "Offset Flag" is a QC metric that is found in the Analysis Dashboard for OncoScan products. This QC metric lets us know if the TuScan algorithm detected that the usual normalization method was off, and therefore required readjustment.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
What data files are produced during the assay and analysis process?
These data 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.
xxCHP file - This file is the output of ChAS 3.1 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 v2.0 and higher).
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What is the difference between OncoScanCancerGeneOnly.r1 and OncoScanGeneBoundaries.r1?
OncoScanGeneBoundaries.r1 lists the approximately 900 OncoScan cancer genes and includes greater than 10 kb on each side of the gene. OncoScanCancerGeneOnly.r1 lists the same approximately 900 OncoScan cancer genes using the start and stop positions of the gene (no additional 10 kb on each side of the gene).
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What does "low diploid flag" mean?
The algorithm identifies normal diploid markers in the cancer samples. This is particularly important in highly aberrant samples. The normal diploid markers are used to calibrate the signals so that a log2 ratio of 0 (e.g., copy number 2) is achieved. In about 2% of samples, the algorithm cannot identify a sufficient number of “normal diploid” markers, and no normal diploid calibration occurs. This event triggers “low diploid flag = YES.” In this case, the user needs to carefully examine the log2 ratios and verify that re-centering is necessary.
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What is "celpaircheckstatus," and what does it do?
Celpaircheckstatus checks if the results from the AT channel are consistent with the results from the GC channel and represent the results of the respective channel. This metric will be “out of bounds,” for example, when the AT and GC channels were mispaired between samples or due to sample contamination. We recommend troubleshooting as described in the OncoScan Console User Manual.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
