I was wondering if anyone could help me. Some time ago I analysed a large time-course two-colour cDNA microarray data set using LIMMA. I followed, to the letter, the instructions in Chapter 9 of the LIMMA user's guide on how to analyse two-coloured data as single channels. I have recently submitted a manuscript for publication that analyses this data and one of the reviewers would like to see my data submitted to the Gene Expression Omnibus (GEO). I attempted to do this, but the GEO curators would like me to submit the normalised single-channel values for each time point (i.e. not ratios). Is there away of obtaining these values? I have no trouble getting M-values between two time-points, but cannot work out how to get the individual time-point values. Your help with this would be greatly appreciated!!!

I'm not an expert in two-colour analyses, but the most obvious approach would be to just extract and report the red/green intensities from each array. Assuming you have a background-corrected and normalized MAList object called norm.MA, you can call

norm.RG <- RG.MA(norm.MA)

to get the equivalent red/green intensities. You can then pull out norm.RG$R and norm.RG$G as necessary.