Hi All, Not strictly Bioconductor question I'm afraid. Is there any reason why we couldn't hybridise 2 samples to one array (1 green, 1 Red) and then perform single colour analysis on both samples independently? It would be a custom agilent array using the probe set from their whole human genome array. Many Thanks Elliott This message has been scanned for viruses by BlackSpider...{{dropped:3}}

elliot harrison wrote: > Hi All, > > Not strictly Bioconductor question I'm afraid. Is there any reason why > we couldn't hybridise 2 samples to one array (1 green, 1 Red) and then > perform single colour analysis on both samples independently? It would > be a custom agilent array using the probe set from their whole human > genome array. People do this, yes. I do not know how much crosstalk between channels there is on modern arrays. You will want to think a little about normalization, also. See the limma user guide for some examples of one-channel analysis of two-color data. Sean