User guide

Data quality flags 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 flag
is shown if the data meets all quality thresholds.
• (yellow) – Review of the analysis results is suggested. This flag is shown if the:
–
Instrument cannot clearly identify the population of unamplified wells.
– Distribution of unamplified wells on the chip is not uniform.
– Sample concentration is outside the optimal range (200-2000 copies/μL) for
the system as currently defined by the chip quality metrics.
•
(red) – Review of the analysis results is strongly suggested. If necessary,
reimage the Digital PCR 20K Chip
or rerun the sample. This flag is shown if the
total number of filled wells is < 5000 or the percentage of low quality wells (those
with well quality < 0.5) is > 25%.
For each QuantStudio
®
3D Digital PCR 20K Chip it reads, the QuantStudio
®
3D
Digital PCR Instrument stores the processed imaging data and the results of the
preliminary analysis to a single experiment (.eds) file.
The instrument names each experiment file 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-specified
text.
2
Date stamp – The date at which the Digital
PCR 20K 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
Digital PCR 20K 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 label applied to the
QuantStudio
®
3D Digital PCR Chip Case
Lid that uniquely identifies the Digital PCR
20K Chip to which it is applied.
X0300036
Chip ID
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 file.
Note: In the example shown above, the file name indicates that the file contains data
for chip BO498N which was run at 7:58 pm on May 31, 2013.
Following an image analysis, the QuantStudio
®
3D Instrument transfers the
experiment (.eds) file for the QuantStudio
®
3D Digital PCR 20K Chip
to the selected
destination and saves a copy of the file locally to the instrument. You can access
and/or download the experiment (.eds) files of previous runs from the Run History
screen.
About data quality
flags
About the data
files
Chapter 4 Analyze the Prepared Chips
Analyzing the data
4
QuantStudio
®
3D Digital PCR System User Guide 75