Hi, 

I am using a two color microarray. After normalization I get values for M and A but I am looking for a single normalized expression value for each gene that you find with single color microarrays. Does anyone know how I can do so?

Thank you!

Check out the RG.MA function. This will return the unlogged red/green intensities from a (normalized) MAList object that contains M- and A-values. Okay, so this isn't a single value, but it's not obvious how you would otherwise summarize a two-colour result into a single statistic. Note, if you want to do a more rigorous separate channel analysis of two-colour data, check out Chapter 12 in the limma user's guide.

Hi SSK,

I'm a bit worried what you are planning to do with the separate channel results. Two colour microarrays are innately competitive. It isn't usually correct to try to reverse back from M and A values to single channel expression values.

If your experiment has a common reference sample (same sample hybridized to Cy3 for all arrays for example), then you can treat the M-values more or less as you would log-expression values from a single colour technology. So, in that case, the M-values may be what you're after.

Thank you for your answers. I am a bit confused. I am trying to do something similar to this paper:

http://www.ncbi.nlm.nih.gov/pubmed/8944026

It seems as though they just use a red/green ratio and compare this ratio across a subset of genes. Does this make sense?