I've ran several idat files of microarray data through lumidat, including the example idat files provided in the lumidat package. The "Detection" column always has it's greatest values (i.e. values at or close to 1) for the probes having the strongest signal strength. For example, below I paste output for the three probes having the strongest signal in the lumidat example idat file 5356583020_A. This output was generated using the example given in the lumidat vignette: example(preprocess.illumina.idat)
I have Genome Studio output for some of the idats that I have run. There are minimal changes in the ranking of probes according to signal strength but the Genome Studio "Detection Pval" for the strongest probes is usually close to 0. This makes sense to me: except if I've misunderstood something, the probes with the strongest signal would be the most confidently detected and thus have the lowest detection p-values. So, why is it that lumidat gives a "detection" value close to 1 and not close to 0? Is the lumidat "Detection" column intended to represent the detection p-value, or does it represent something else? (e.g. detection type 2 error, which I guess is 1-p?). Also (and more importantly) is this difference between Genome Studio and lumidat automatically accounted for in downstream workflows such as Lumi?
edit: I should add that the title may be a little misleading because the lumidat "detection" value is not precisely 1-x of the "detection_pval" given by GenomeStudio - it is approximately 1-x, in the examples I have checked.