What does the black square or the black cross in the Fluidigm RT PCR Analysis software HeatMap mean?

The black square denotes Ct values of >40 or <1, indicating a failed reaction. An air bubble or obstruction in the microfluidics can give an error of this kind. A black cross is shown if the amplification curve deviates too much from an ideal amplification curve. Look at the amplification curve for another sample for the same assay and compare the curves and the Ct values. If they seem very different, exclude the failed/crossed sample for that assay. If they are very similar, ignore the failed/crossed sample.

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