[BioC] P calls (VSN and RMA)

[Petra B Ross-MacDonald]

I agree there would not be a universal value for the transition point - I
think that's why in this experiment, twelve B subtilis probesets that
shouldn't hybridize can give intensities as high as 7.9, and six BioB
probesets that should hybridize give intensities as low as 7.4. This is the
region that Naomi talked about, where some low level mRNAs are giving the
same values as some absent mRNAs.

I'd also expect these overlap values to shift around somewhat with every
experiment batch processed with VSN (since I have seen absolute values in
for some genes control samples jump quite a bit in different projects). But
within one dataset, it seems these negative control probesets provide an
indicator of where the region is, and allow you to make decisions about
which probesets to throw out if you want to use a False Discovery Rate
metric. You could make a cut low in the region for sensitivity, or high for
selectivity. In Naomi's case, if you really care about identifying low level
RNAs that are upregulated by a small amount, you could run the ANOVA to
identify genes of interest without the cut, but run it again with the cut to
get a better idea of what the p values really are.

I am going to try and find out more about the control spots. The Affy site
doesn't have anything obvious about using them.

Cheers, Petra


w.huber at dkfz-heidelberg.de wrote:

> > Thus, the transition between sensitivity and selectivity occurs at
> > intensity values between 7.4 and 7.9.
>
> From what other people have told me, I'd expect that there is not a
> universal value, but that it would be different for different probe
> sequences (according to the distribution of C, G, T, and A across the
> positions 1..25). Also, the exact value would depend on scanner settings
> etc. .... Opinions?
>