[BioC] Intensity distribution of "significant genes"

[Naomi Altman]

On an Affy array the genes are represented by probes which are supposed to 
be spatially dispersed on the array.  So, to visualize the locations of 
differentially expressed genes, you need to extract the locations of all of 
the probes.

Supposing you have this information, you could divide the array into say 4 
"rows" and 4"columns" and do a 2-way ANOVA using the probes as replicates.

Alternatively, and informally, you can use "image(rawData,col=rainbow(6))" 
to obtain a color image of all of the probes.  "Blops" on these plots 
indicate a hybridization problem - but they need to be large to really 
affect your inference about gene expression.

--Naomi

At 01:53 PM 1/21/2004, 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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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111