Hi again Neil,
You should first import the data into J-Express by choosing "file" -> "load raw data". Drag and drop the two gpr files into the "experiment design table".
Choose the channel1 and channel2 (F635nm - B635nm and F532nm - B532nm).
set the "Combine in-array replicates" to NO and make sure "Result data" is set to none.
Then select an array (click an array icon) and click the process tab. Add appropriate filters (for controls etc.) and normalization if needed (e.g. a global lowess normalization). copy the processes to both arrays by clicking the "copy to all" button.
click compile to create a expression matrix.
You should now get a 4 column dataset.
select the dataset and open the script window from the menu "dataset" (select pyton script window)
I created a script which can be found on the forum at:
http://molmineus.com/forum/index.php?topic=60.0copy all script code and paste into the empty script window.
look through the script and see my comments.. verify that the script does what it should.
click the execute button.
If I understood the data layout correctly, the script should produce the results you want.. We can add other statistics later if you want..
Bjarte.