Search Thermo Fisher Scientific
Having difficulties with your experiment?
We are dedicated to your success. Get back on track. View our expert recommendations for commonly encountered problem scenarios.
View the relevant questions below:
Beginning your experiment?
Visit our
Many problems with OpenArray plate results can be diagnosed by examining the QC images taken at various points during a cycling/imaging run. In the QuantStudio software, with the experiment in question open, click on “Export QC Images” in the Export tab. A set of images will be exported to the chosen folder location. Note: Export a set of images to a unique folder, as exporting another run to the same folder will overwrite the images.
The images exported are either fluorescent or reflected light images taken before, during, and after cycling. Real-time and SNP runs will produce somewhat different sets of images, though the ones useful for troubleshooting are easily identifiable in each set.
Image Name | Description |
BARCODE IMAGE.tiff | Reflected light image of the entire OpenArray plate, useful for confirming the identity of a folder full of images |
PRE-READ_CHANNEL_4.tiff | Pre- and post-ROX™ dye images, useful for assessing the loading quality |
s00_c001_t01_p0001_m2_x3_e1_cp#_spotfind.tiff | Pre-run reflected light spot-finding image (used by the software for determining the location of the holes), useful for checking for existing contamination on the case and/or heated cover |
s02_c001_t03_p0001_m1_x2_e1_cp#_spotfind.tiff s03_c001_t03_p0001_m2_x3_e1_cp#_spotfind.tiff | Mid-run reflected light spot-finding image, useful for identifying potential leaks or other contamination that only appears mid-run |
s99_c001_t01_p0001_m4_x5_e1_cp1_spotfind.tiff | Post-run reflected light spot-finding image, useful for identifying potential leaks or other contamination |
STAGEx_CYCLEy_CHANNEL_z.tiff | FAM™ (z=1) or VIC (z=2) dye images at a particular cycle (y) of a particular stage (x) of the run, useful for looking at patterns in the fluorescent data (e.g., gradients) |
To view images, a free imaging program called ImageJ is recommended due to its ability to easily manipulate the images in ways that programs such as the built-in Windows image viewers can’t. Many images will need to be adjusted for brightness/contrast in order to really be able to see what is happening. To do this, open the image in ImageJ, then open the brightness/contrast adjustment via ImageàAdjustàBrightness/Contrast (or press Ctrl+Shift+C). Then, simply click the Auto button (or adjust the sliders) until the features of interest in the image are visible.
Please follow the instructions below on how to clean the block.
Note: This screen is only present when the OpenArray sample block is installed.
Go to C:\Documents and Settings\yourname\Local Settings\Application Data\Applied Biosystems\OpenArray AccuFill™ System. Then delete Instrument.log and OpenArray Plates History.csv. Note that this will remove all loading history, so you may want to save it elsewhere.
Try transferring the file again. If that doesn’t work, use a USB stick to collect the results from the instrument console and transfer it to the computer from the USB stick. If you are still unable to open the file, please call technical support and be ready to email the .eds file as well as the log files.
Extract the QC Images using the QuantStudio software. Navigate to the folder where they were saved, and open the PRE-READ_CHANNEL_4.tiff and/or the POST-READ_CHANNEL_4.tiff files. These are the ROX™ images, so any missing through-holes are easily seen. See page 95 of the Pharmacogenomic Experiments User Guide.
Occasionally there may be probe cleavage and the NTC will cluster with the samples. First, check that not all the other assays in that subarray are affected. If all the other assays show the NTC clustering with samples then there may have been a sample tracking issue and it is not really an NTC. If all other assays in that subarray show NTC where expected, then check the amplification curve in the QuantStudio software. Compare the Ct values of the NTC sample compared to the Ct values of samples. The NTC Ct values are high. So the probe has undergone cleavage but the signal is late and since the genotyping assay is an endpoint result, the NTC is shown to cluster with the samples. You can analyze using the “Reveal Traces” feature in QuantStudio software, or import into Genotyper™ software to review the scatter plot at a lower cycle, before the spurious cleavage has occurred.
This means that the analysis software was unable to definitively assign a genotype call. This can be due to a number of factors including: a neighboring SNP, copy number variant, or sample quality issue (e.g., sample degradation, or the presence of impurities in the sample). If the result falls between two clusters, you should not assign a genotype call. These types of results would typically be characterized as “undetermined.” You can review the amplification curves and/or the real-time traces to check for “noisy” data, which can confirm these “bad” results.
You can download an example translation table from here. Use these examples as a template, and populate the corresponding assay and allele information for your assay of interest. This new file can then be imported into AlleleTyper™ Software.
No, it is not possible to determine the strand from the assay data. However, this information is typically not necessary.
Check the web browser you are using. AlleleTyper™ Software is accessed as an internet application that is optimized for use with the Microsoft Windows operating system running the Google Chrome™ web browser v4.0 or later.
Check your table against one of our example tables to make sure the format is the same. For the calls, make sure you only have the bases listed that are possible for that assay. For example, if an assay is for an A/G SNP, if you have a T or C in the table by mistake then the file will not import.
Make sure you are exporting from Genotyper™ using Advanced mode.
For Research Use Only. Not for use in diagnostic procedures.