Dear List,

I had posted earlier about my problem but didn't get any response that could
help so I am seeking your help again.

I have duplicate spots on my nimblegen array that are position randomized so
there is no order to their placement. In Limma when we call the
duplicateCorrelation() function, it requires that the duplicate spots have
some order to them, like they are either adjacent or they are on upper and
lower halves of the array. In this case, can someone please help me about
how to go about analyzing these spots?

I really appreciate your input.

Sincerely,

Vishal

Code:

corfit=duplicateCorrelation(ma.quantile, ndups=2)

This gives me a negative corelation of -0.08 the reason being that the spots
are randomized. Is there a solution to this?

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