missing data in ChromHMM

Question

[luminea]

I am currently working with ChromHMM and am seeking clarification regarding the "missing data" entries labeled as "2" that appear after the binarization of the BED files. Shouldn't we expect to see 0s instead of "missing data" when no signal is detected in the BED files? Thank you for your assistance!

[LChart]

Did you happen to segment a single track, rather than multiple tracks? I seem to recall the "missing data" is for when no track has any signal.