Thank you for your reply, Dr. Smyth.

I do not yet completely understand exactly HOW normalizing works (I've seen
the data, transformations, and so I know what it does, just not how, yet)
but it appears to me that I can simply change the sign of the normalized
output to make the proper tests (or as someone else stated, reverse the
contrast / estimate statements).
You picked up on my motivations here - I am chiefly concerned that the
exported normalized data has proper signs because at present I am required
to do all of my linear modeling in SAS, and large datasets need to be 'read
in.'   I personally would rather do it all in R which is why I am running
things in parallel to make the case for limma-only analysis.

You people are both programmers and teachers, and thanks for your patience
with the noobs.

AM

	[[alternative HTML version deleted]]

