[BioC] help in 2-color data normalization

[Jeremy Davis-Turak]

Hi Jianping,

> In terms of my previous question of whether or not they could be "real"
> difference existing between the colon cancer and the universal cancer cell
> line RNAs, considerations may be given beyond just removing those spots.
> What I noticed was that some probes can only be hybridized with the
> reference RNAs and some others only with colon cancer samples (see
> "RG_cutoff.jpeg" at <http://www.unc.edu/~jjin/Graph/> ). Take one chip as
> an example, 4548 genes showed  green signals more than 2^8 with read
> signals less than 2^6, and 1831 genes showed read signal more than 2^8 with
> green signal less than 2^5. On both cases maximum signals, read or green,
> can be as high as 2^12. The observation suggested that there exist some
> real differences between RNAs.

If these differences you see are really due to differences in the cell
types, you should see the reverse effect in the dye-swapped arrays.

You may also want to have a look at the raw signals, and also check
the quality of the slides (just because the slides are Agilent doesn't
mean they're perfect).

Jeremy Davis-Turak