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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_whitepape r.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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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