[BioC] Simpleaffy QC & GAPDH ratios

[Lana Schaffer]

Saroj,
Thank you for your pdf reference.
I know what is generally written about these GAPDH ratios, but
the ratios from Simpleaffy have never made sense.   
First, these ratios are not the same as the ratios from the Affy
software or from calculated Mas5.0 ratios.  
Second, there are not only ratios between 0 and 1, there are also
negative ratios.
Third, the only way this makes sense, is that these are log ratios.

Lana 

-----Original Message-----
From: Saroj K Mohapatra [mailto:saroj at vt.edu] 
Sent: Friday, June 12, 2009 10:03 AM
To: Lana Schaffer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Simpleaffy QC

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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