Thermo Scientific Applied Biosystems QuantStudio - Data Quality Flags; About Data Files

Data quality ags generated and displayed by the software are a measure of the
overall chip quality, based on well quality thresholds and other data analysis
characteristics.
Note: For more information on quality assessment in the software, see the user
documentation for the QuantStudio
™
3D AnalysisSuite
™
Software.
In order, from high quality to low quality:
•
(green) – Review of the analysis results is suggested, but not required. This
ag is shown if the data meets all quality thresholds.
•
(yellow) – Review of the analysis results is suggested. This ag is shown if the:
–
Instrument cannot clearly identify the population of unamplied wells.
–
Distribution of unamplied wells on the chip is not uniform.
–
Sample concentration is outside the optimal range (200-2000 copies/µL) for
the system as currently dened by the chip quality metrics.
•
(red) – Review of the analysis results is strongly suggested. If necessary,
reimage the chip or rerun the sample. This ag is shown if the total number of
lled wells is < 5000 or the percentage of low quality wells (those with well
quality < 0.5) is > 25%.
For each chip, the QuantStudio
™
3D Digital PCR Instrument stores the processed
imaging data and the results of the preliminary analysis in a single experiment (.eds)
le.
The instrument names each experiment le uniquely by combining the ID of the chip
and the date/time of the run according to the following formula:
2 3
1
4
1
File prefix—The optional user-specied text.
2
Date stamp—The date at which the chip was run, expressed in the "yymmdd" format where
yy is the last two digits of the year, mm is the numerical order of the month, and dd is the day
of the run.
3
Time stamp—The time at which the chip was run, expressed in the "hhmmss" format where
hh is the hour (in 24-hour format), mm is the minutes, and ss is the seconds.
4
Chip ID—The number on the chip lid and encoded in the 2D barcode that uniquely identies
the chip.
443MPJ
IMPORTANT! If the instrument cannot read the ID of a loaded chip, then it uses the
date/time of the run instead to name the le.
Note: In the example shown above, the le name indicates that the le contains data
for chip BO498N which was run at 7:58 pm on May 31, 2013.
Data quality
flags
About data
files
Chapter 5 Image and analyze the chips
Primary analysis
5
48
QuantStudio
™
3D Digital PCR System User Guide