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KB005443: The default cut-off value for the "Present" gene is 0.8-GeneSpring GX
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For Illumina data, if the flag value is based on the detection P value, the "Present" gene should be the detection P value < 0.01. However, the default cut-off value for the "Present" gene is 0.8 in GeneSpring GX. Why?
The actual values in Detection p-value column of BeadStudio will show the p-value as, the lower the number the higher the confidence that this gene is being detected. It functions as a p-value.
The value from the GeneSpring format file (when you export the data in GeneSpring GX format) exports a Detection value. It is the equivalent of 1 – value (for example: 1- 0.001=0.9999). Therefore, the closer the number is to 1 the better it is.
The numbers are different because these are different metrics/functions.