Probe filtering software tools | DNA methylation microarray data analysis
Several reasons can explain the generation of artifactual data. For example, the scanner can encounter some difficulties to correctly read the signal for some probes owing to their low intensities or to some spatial artifacts on the array. This problem translates as a high detection P-value (i.e. a low quality signal) for the probes concerned. It is therefore strongly recommended to filter out probes displaying a high detection P-value (e.g. >0.05) before performing downstream analyses. This problem is common to all microarray platforms.