Graphs & Optical FAQ

Q: What dyes can be used on the SmartCycler®II System?

A: The SmartCycler® II System is calibrated for FAM, Cy3 or TET or Alexafluor532, Texas Red and Cy5 or Alexafluor647.

Q: Can I use VIC, HEX or JOE on the SmartCycler®?

A: VIC, HEX, and JOE are very similar to TET and therefore may work with our calibration, but we cannot guarantee their performance since the base it is attached to may shift the optical spectrum. To use a dye that has not been calibrated at Cepheid, we suggest running as a simplex reaction and viewing the fluorescence reading in the adjacent channels to determine any cross-talk. If the desired result is not generated, the SmartCycler® and SmartCycler® II system may be recalibrated with the user-defined Optical Calibration feature in the SmartCycler®Software.

Q: I created a FAM graph but it is displaying temperature.

A: This is most likely due to the incorrect graph type. Check the graph definition in the Define Graphs screen to verify that the graph type is optics and not set to temperature.

Q: I created a new graph but it is not listed in the View Results screen.

A: When a new graph is defined in the Define Graphs screen it is saved and stored in the database but not associated with a run unless the "Automatically add to new runs" box is checked. To view a new graph, go to the View Results screen and click the Select Graph button at the bottom of the screen. Highlight the graph name in the "All Graphs" column, click the right-pointing arrow then click OK.

Q: When I use the print icon, the graph print out does not contain enough information, is there an alternative way to capture a picture of the data?

A: To capture the entire screen use the Print screen button on your keyboard. Simultaneously hold down the Print Screen and Alt buttons on the keyboard then open Word or Power Point and select paste.

Also, it is possible to save the screen as a jpeg file and to save graphs as jpeg files. To save the screen as a jpeg file go to the Tools menu and select Save Screen to File. To save a graph as a jpeg file, right-click on the graph and select Save to file(jpg).

Q: I can't zoom on a graph when a run is in progress.

A: Since data is constantly being collected and reported in real time, it is not possible to hold a zoom from a previous time point. This occurs even when viewing a saved run if another run is in progress.

Q: How can I get negative fluorescence?

A: This is caused by the background subtraction calculation. This usually occurs when the threshold is set too high. If the primary signal or 2nd derivative does not cross the threshold, the background subtraction calculation will continue until the end of the run. Try decreasing the threshold value or adjusting the background min and max values.

Q: Do I need to select graphs before I start a run?

A: It is not necessary to define or select graphs before the run is started. Graphs can be created before, during, or after the run is started.

Q: Can I look at other runs while the instrument is in use?

A: Yes, it is possible to view and analyze previous runs while the instrument is in use.