Hello, I have data from four dual-color microarray chips, but something gone wrong with last one. Only one dye is active. Probably second dye wasn't placed. Of course this last chip must be excluded from further experiment analysis. However I'm curious about way to analyse such data and compare it with first three chips. Is there any chance for doing it? What do you think about this?
In principle you can use the R- and G- signals from the arrays as separate measurements (as if you did 7 single-color arrays). The paired structure can be accounted for with a mixed model ("array" must be a random effect because one partenr is missing [the last one where one dye failed to give a signal]). It depends on the arrays if the paired analysis is reasonable (it only is when the array quality is rather low: irregular spots, different sizes and so on - often typical for self-made chips and cDNA-chips, not so for most commercial chips).
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