[BioC] Intensity distribution of "significant genes"

[Rafael A. Irizarry]

for  cDNA this is easy. there are some functions in the packages for 
cDNA, e.g. in maImage in marrayPlots.

but with affy the problem is that genes dont have locations. each of the 
11-20 probes have a location. would you like to see the location of the 
probes for each gene? the function plotLocations can be used for this.


 On Wed, 21 Jan 2004 Phguardiol at aol.com 
wrote:

> Hi all,
> this a pretty general question ...
> let say I have identified a set of genes differentially expressed between 
> group A and group B and I m using Affy chips (but this could be also interesting 
> for 2 color arrays). 
> Is there a way - something already available) to see the distribution of 
> these down and up-regulated genes (with 2 different colors) on the chip slides ? 
> In addition, if we have "the impression" that the 2D distribution of these 
> spots is not random with, for instance, a high density of these in the "left up 
> corner" or somewhere else, is there a statistical test - so that it is no more 
> an impression - to say that in some parts of the image, the distribution of 
> these differentially expressed genes does not seem to be random suggesting a 
> problem with the procedure or the slides ? I think that looking at the slides is 
> necessary but not enought... ?
> Hoping that all this is understandable...
> Thanks
> Philippe
> 
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