[BioC] dependence of log2-ratios on scanning sensitivity?

[Kamila Naxerova]

Hi all,

I am analyzing a bunch of miRNA arrays (Exiqon, dual channel, Hy3/Hy5). I
am confused about the following issue.... Please apologize potential
naivete, I have practically no experience with two-color designs.

The chips have so called "Hy3 landing" lights, i.e. Hy3-labeled capture
probes that help position the array for scanning. The mean intensity of
these landing lights is very different between arrays (I assume that means
slides were scanned with different sensitivity).

First I thought that I don't have to worry about variable brightness among
the arrays - I hybridized the exact same reference to all of them. But
then I computed the correlation of all "real", intra-array normalized
probe log2-ratios with the Hy3 landing light brightness... and the
distribution has a disconcerting peak around 0.5. Am I missing something
obvious?

Thanks a lot.
Kamila