[BioC] Regarding quantile normalization.

[Sean Davis]

On Sat, Jan 1, 2011 at 9:23 AM, Veerendra GP <gpveerendra09 at gmail.com> wrote:
> hellow everyone!
>
> I will be delighted if any one can help me with this! I am working on a
> microarray dual channel data, and i need to do a inter array normalization.
> I have tried with quantile normalization (available in limma package) method
> but the result i am getting is not satisfactory as the boxes are not
> appearing to be of the same sizes which according to the fact should be the
> same. can you please give me a reason for this. and is there any better
> normalization method available for dual channel experiment.

Hi, Veerendra.

If you are doing "separate channel normalization" using quantile
normalization of red and green channels between arrays, then I do not
think there is any requirement that the boxplots of ratios be
identical.  Is that what you mean by "boxes"?  Perhaps I am
misunderstanding what you have done, though.  If you want comments on
the code, then feel free to post as close to a reproducible example as
you can and the output of sessionInfo().

Sean