[BioC] IMAGE PLOTS.

[stephen at iwinet.rug.nl]

Thanks, Laurent. I got the solution by applying plotLocation() command. Using
this one can see that the image plot includes both MMs and PMs. 

Stephen.

Quoting Laurent Gautier <laurent at cbs.dtu.dk>:

> 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.
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> 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
> 
> 
> 
> -- 
> --------------------------------------------------------------
> Laurent Gautier			CBS, Building 208, DTU
> PhD. Student			DK-2800 Lyngby,Denmark	
> tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent
> 
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