[BioC] normalisation assumptions (violation of)

[Sean Davis]

On 8/7/06 6:59 AM, "J.delasHeras at ed.ac.uk" <J.delasHeras at ed.ac.uk> wrote:

> 
> Hi,
> 
> I have a set of data from an experiment where there appears to be an
> effect of the treatment on a large number of genes. I put scatterplots
> for 6 of the slides here:
> 
> http://mcnach.com/MISC/scatterplots.gif
> 
> these are Cy3 vs Cy5, in log scale.
> 
> These show that many genes are differentially expressed, and they are
> mostly one one side only (upregulated; some of those slides are dye
> swaps).
> 
> Would this appear to violate (too much) any of the assumptions made by
> loess normalisation? Should I investigate other normalisation
> procedures?

First, I would start by doing a VERY thorough evalutation of the slide
quality for these slides, as these are very distorted scatterplots.  IF the
slide quality looks OK, then I would probably stay away from a non-linear
normalization method, as these will tend to make your
differentially-expressed genes look less differentially-expressed.

Sean