[BioC] using genomic DNA as universal reference

[Jianping Jin]

Dear list,

I would like to ask comments and suggestions on how to normalize microarray 
data with genomic DNA as reference.

The experiments were performed with bacterial RNA and genomic DNA samples. 
What I noticed was that the data were pretty consistent across all chips on 
both channels.  But there exists a huge difference between the two channels 
in terms of the distribution of the probe intensities, although the average 
intensities were the same for the both channels. T statistics with 
non-normalized data showed that there were two thirds probes with p values 
<= 0.05 by comparing the hybridization intensities between red and green 
channels.

Regarding to the huge difference described above the normalization methods 
people usually use may not be appropriate for the RNA/DNA data sets. What 
normalization algorithms would be useful if there is any? Does anyone have 
experience with this?

Any comments or suggestions will be appreciated!

Jianping Jin


##################################
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