[BioC] help in 2-color data normalization

[Jianping Jin]

Thanks Jeremy,

You made a good point. Unfortunately the dye-swapped arrays were not 
considered in the original experiment design.

We did check the quality of the slides. We found the slide were good except 
a couple of samples which we removed from the analysis due to some gridding 
problems.

thanks again for your comment!

Jianping

--On Saturday, May 12, 2007 11:50 AM -0700 Jeremy Davis-Turak 
<jeremydt at gmail.com> wrote:

> 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
>
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##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu