[BioC] Limma: reading in additional spot data (flags)

[Edo Plantinga]

Dear all,

I would like to use Limma to read in not only the signal and background value, but also to read in additional spot data (spot quality flags, in this case). Our lab uses Imagene for the image processing of slides. Is there any way I can do this without completely hacking the source code and without reading the same files twice? If not, what would be the best way to do this?
Secondly, is there a particular reason why the mean signal is read in into Limma, but the median background is read? I would like to be able to read in the median spot intensities. Again, is this possible without too much hacking?

Regards,

Edo Plantinga
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