[BioC] using genomic DNA as universal reference

[Wolfgang Huber]

Dear Jianping,

I think the following paper (method is implemented in the function
normalizeByReference of the tilingArray package) describes a setup very
similar to yours (using Affymetrix 25mer tiling arrays and with yeast):

Section 2.3 of Huber W., Toedling J., Steinmetz L. M. (2006) Transcript
mapping with high-density oligonucleotide tiling arrays. Bioinformatics
22(16): 1963-1970.
http://bioinformatics.oxfordjournals.org/cgi/reprint/22/16/1963.pdf

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


05/06/2008 17:31 Jianping Jin scripsit
> 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
> 
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