[BioC] maanova background correction

[Brendan M. Heavey]

Hello-

I am using MAANOVA to analyze cDNA chips.  Does anybody know how to 
deal with background spot intensity?

Right now, I have about 4000 genes on an array, each spotted 3 times.  
I can input the raw signal strength for each of the 12,000 spots and 
run analysis on those.

I would like to subtract background intensity from each of the spots, 
but this leads to negative values in some spots (that haven't 
hybridized).  Maanova seems to not like negatives or missing values, 
which means I have to eliminate all 3 spots for each gene that produces 
a single negative...which reduces my dataset to a pitiful number of 
genes.

I've considered:
1). Replacing the missing/negative value with a number very close to 
zero
2). Replacing the missing/negative value with the average of the other 
two spots
3). Forgetting about background intensity completely and just using raw 
signal strength

...but none of them seem like the right thing to do

any ideas?

thanks in advance

Brendan Heavey
Analyst Programmer
Center for Research in Cardiovascular Medicine
University at Buffalo