Hybridization signal variation in DNA array preparation

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LoneProbe
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Hybridization signal variation in DNA array preparation

We seem to be having significant signal variation using the same 5' amine-labeled probe but a different batch of EDC when conjuating probes to COOH solid support. Usually an older batch of EDC gives higher hybridization signal than a new batch.

Does anyone see an equivalent phenomenon? One idea we are pursuing is perhaps probe density with a new EDC is higher than with an old batch, thus lowering hybridization signal. Also we cannot exclude conjuation at non-5' amine within an oligo.

Any comments will be appreciated.