GenomeStudio Methylation Module why are some beta values blank even though there are intensities reported for them?

In GenomeStudio Methylation projects, some Beta values are blank even though there are intensity values reported in the Signal A and Signal B columns. The reason usually is that the number of beads used to calculate an intensity falls below the threshold of 3 for either the red channel or the green channel. If either the intensity from signal A or signal B is calculated from less than 3 beads, then GenomeStudio will not calculate or report a Beta value.

In order to confirm this, the user should add the subcolumns "Avg_NBEADS_A" and "Avg_NBEADS_B" to the Sample Methylation Profile,

then sort the Avg Beta column A-Z for a single sample. Avg_NBEADS reports the number of beads used in calculating the reported signal.

The blank Beta values will appear at the top. For these markers, the user will find one or both of Avg_NBEADS_A or Avg_NBEADS_B will have fallen to less than 3. Note that there is no way to bypass this threshold in GenomeStudio, so if the user wishes to calculate a beta value for such assays, they will have to do so manually outside of GenomeStudio.

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