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I'm sorry if this is a stupid question - I have not analysed two channel array data before.

I have a GenePix data file, which does not seem to indicate which channel (red or green) is used as reference channel.

If it possible to tell this from the data itself?

Where raw is my data object, and G is a dataframe of the green channel data and R is the data frame of the red channel data, the ranges are as follows:

#range(raw$G)
[1]    45 21939
> 
> range(raw$R)
[1]  39 332
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No, you can't get this from the data itself. If there is a control/reference sample on one channel, you need someone to annotate which channel it's on.

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