How does one take two 96 well plates I and II with wells A1-H12, and batch them such that A1-I is batched with A1-II, B2-I/B2-II .. H12-I,H12-II ? (let's call this state "lined up")
Easy way:
1. if you annotated the WELL POSITION keyword, add it to the workspace as a column.
Mac: Workspace menu/Edit workspace columns
PC: Workspace menu/Edit Columns
2. Double-click that column header to sort by its value. They should now be "lined up".
3. Open the Layout Editor. Click Layout menu, Iteration Options. Set it to 2 tubes (assuming you want to compare two files at a time, ie. A1-I vs A1-II)
4. Bring in A1-I and A1-II and align them as you want them, including side-by-side, grids, overlays.. etc.
5. Batch - new layout will be created, where each tile compares one well from plate1 to the equivalent well of plate2.
Medium way
Oh well, you didn't label wells into keywords. But at least the plate wells are in chronological order, ie.
1. plate1-A1
...
96. plate1-H12
97. plate2-A1 etc.,
all we have to do here is create a new blank keyword and fill it with a numerical series to "simulate" well position labels. Both are easily done on Mac and PC:
1. workspace menu/add keyword. call it anything you want. I called mine "well".
2. double click the "well" cell across the first FCS file (A1). It should become active.
3. While your cursor is blinking inside the well cell, option-click the Workspace menu and choose "create value series" (note kb shortcut option+cmd+E)
4. leave Staring Value, Increment, Multiplier and Replicate Value at 1. Set the "Star Over every.." field to the number of wells in ONE plate (ie. 96)
5. click OK
6. double-click on the "well" column header, files should be "lined up".
7. continue from step "3." in above paragraph.
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