Say one file is called a.tif and the other b.tif. The channels of interest are both called Alpha 1. Say we're working on Windows.
In a.tif
- Select Alpha 1 by clicking on channel in Channels window
- Select All (Ctrl-a)
- Copy (Ctrl-c)
- New File (Ctrl-n). Call this file c.tif
- In new file Paste (Ctrl-p) Call this layer A
In b.tif
- Select Alpha 1 by clicking on channel in Channels window
- Select All (Ctrl-a)
- Copy (Ctrl-c)
- In c.tif Paste (Ctrl-p) Call this layer B
In c.tif
- Right click on the top layer
- Blending options... | Difference
c.tiff will be completely black (value 0) for all pixels if layer A and B are identical. You can check this either by scanning across with your mouse and using the Info window. Or by applying Image|Auto contrast to each layer one at a time.