[BioC] Calculating microarray ratios between channels from different arrays

[michael watson (IAH-C)]

Hi

I wondered what the list felt about calculating ratios between channels
from separate microarrays?

Let me explain.  I have come across an experiment (not designed by
myself) where I have the following:

+ve cell lines - cell lines with random genomic insertions that display
a +ve phenotype
-ve cell lines - cell lines with random genomic insertions that display
a -ve phenotype
Parental cell lines with no genomic insertion

Now to me it would have made sense to compare +ve vs parental and -ve vs
parental to find those genes which are present in the insertions but not
in the parent which may be contributing to the phenotype.

However, the experimenter did not do this;  they compared each +ve cell
line to the -ve cell lines, and also the parental cell lines to the -ve
cell lines.

So intuitively what I want to do is calculate ratios of +ve/parental and
-ve/parental for each of the experiments, when what I have is +ve/-ve
and parental/-ve.

Is it valid simply to take the (single) list of values for the parental
cell line and use that repeatedly as the denominator for the +ve and -ve
channels from the other arrays?

Thanks
Mick