[BioC] using genomic DNA as universal reference

[Jianping Jin]

Dear Wolfgang,

It is an interesting model for DNA reference normalization. I will take a 
look at it in details.

Thanks a lot!

Jianping

--On Friday, June 06, 2008 10:10 AM +0100 Wolfgang Huber <huber at ebi.ac.uk> 
wrote:

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