[BioC] IMAGE PLOTS.

[Laurent Gautier]

On Wed, Jan 21, 2004 at 09:04:16PM +0100, Stephen Nyangoma wrote:
> Hi all,
> I am doing image plots of affy chips but cannot get a good refference
> for interpretations. I have read the manual but all it says is that you
> can examine the quality of the intensities from it. It does not explain
> what is plotted, for example. Does the image plot depict both PM and
> MMMs or just PMs. Are the intensities log transformed? How is it
> constructed? Is it realted to the hist plot (which is just a histogram
> of the logged PM intensities on a chip)?
> 
> Thanks for your help.
> 
> 
> Stephen.
> 
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The images are simply probe intensities at their respective X/Y coordinates.
The intensity are encoded by colors. *all the probe intensities* in CEL
files are plotted (PM/MM/unknown). One can specify a transformation to
apply on probe intensities prior to color encoding. If I remember right,
the default transformation was set to 'log' not so long ago. The default
coloring is a grey scale.

Examples of such image plots showing experimental artefacts can be found
in Chapter 4 of 'Analysis of Gene Expression Data, Methods and Software'
(Springer), or in the forthcoming article 'affy - Analysis of Affymetrix
GeneChip data at the probe level' (Bioinformatics, Feb. 2004).


Hoping it helps,



Laurent



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