[BioC] Simpleaffy: how are 3/5 ratios calculated

[Ganiraju Manyam]

Hello,

I am currently looking at the simpleaffy package for affymetrix data QC.
I have a question regarding the 3'/5' ratio reported in the graph and by
the function "ratios"

This ratio is different from the ratio obtained by using the value reported
by the qcProbes() function and making the division "by hand".

Even I see negative ratios. Using the data from qcProbes(), i guess negative
ratios are not possible.

Can some expert elaberate the background process going on here?

Thanks for your time.

Ganiraju