[BioC] Simpleaffy QC

[Saroj K Mohapatra]

Hi Lana:

"GAPDH 3’:5’ values are plotted as circles. According to Affymetrix they 
should be about 1. GAPDH values that are considered potential outliers 
(ratio > 1.25) are coloured red, otherwise they are blue." -- 
http://bioinformatics.picr.man.ac.uk/downloads/QCandSimpleaffy.pdf

I think the color of the 'circle' symbol matters more than its actual 
position; red suggests a ratio > 1.25. The x axis labels refer to scale 
factor.

Best,

Saroj

Lana Schaffer wrote:
> Hi,
> The plot(qc) command prints a plot of the Affy QC metrics.
> The GAPDH ratio is a bit confusing because the ratios
> range from <0 to >3.  How can the GAPDH ratio be 0?
> Could these values represent log of the ratio?
>
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu 
>
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