[BioC] using genomic DNA as universal reference

[Sean Davis]

On Thu, Jun 5, 2008 at 12:31 PM, Jianping Jin <jjin at email.unc.edu> wrote:
> 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?

While not ideal, this sounds like a common reference design.  You
could make use of normal two-channel normalization methods (centering,
linear, or loess, etc.), use only single-channel data (and ignore the
control), or use some of the single-channel normalization methods for
two channel data described in the limma user guide.  I'm not sure that
the t-test results are that important in making a decision.  Others
might have more insight and (more importantly) more experience in this
situation.

Sean