Dye swap replicates

[micro123]

Hi,

Hopefully someone can advise me on this.

I'm returning to an analysis of a ChIP-chip that was thought to be unsuccessful at first, but it's looking like it actually could be quite interesting. The only problem is, I've moved labs now and have no way of checking the dye swap orientation. My instinct is normally as follows:

Sample 1: Input - Cy5, ChIP - Cy3
Sample 2: Input - Cy3, ChIP - Cy5
etc

but looking at the results, I am beginning to doubt that orientation and am thinking it could be the inverse.

Is there any way of checking which is which by looking at any raw data values? I'm assuming that the input samples will fluoresce more spots on the array than the IP sample, so is there a way of checking that? Or would the channel with the input have a mean higher signal? I'm not sure...any help would be greatly appreciated.

Unfortunately, my old lab have misplaced my lab book so there's not an easier option....

Thanks again