[BioC] MAS5 statistics

[James W. MacDonald]

Hi Tony,

Brooks, Anthony B wrote:
> Hi all,
> 
> I know it's possible to get some "MAS5.0" stats generated in
> Bioconductor (such as AvBG, %P etc..) 
> 
> What I'd like to do is get the "Background Standard Deviation" and
> "Signal (All)" as it appears in the Affymetrix Report file.
> 
> Is this possible through BioConductor?

This reminds me of one of my favorite fortunes:

 > library(fortunes)
 > fortune("Yoda")

Evelyn Hall: I would like to know how (if) I can extract some of the
information from the summary of my nlme.
Simon Blomberg: This is R. There is no if. Only how.
    -- Evelyn Hall and Simon 'Yoda' Blomberg
       R-help (April 2005)


So the real question here is how does MAS5.0 calculate the "Background 
Standard Deviation" and "Signal (All)"?

The first one seems pretty obvious, and there is a method in the affy 
package to subtract the background (bg.correct.mas()). It would be 
pretty simple to hack that function to get the background that was 
subtracted and then compute a standard deviation.

Which leaves us with 'Signal (All)'. I took a cursory glance at the sadd 
whitepaper

http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf

and didn't see anything obvious. If you can tell us what this is and 
preferably how it is calculated, then we could probably tell you how to 
get to it.

Best,

Jim


> 
>  
> 
> Tony
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623