[R] SAM analysis fold change output

From: Nikhil Garge <ngarge_at_mail.mcg.edu>
Date: Thu 04 May 2006 - 03:34:30 EST

Dear R users,  

I am have a question on SAM analysis - two class unpaired. I am not sure how exactly SAM calculates the fold change for logged2 transformed data. The output produced by SAM -
rbind(siggenes.table$genes.up,siggenes.table$genes.lo) - has numerator, denominator, d-statistic, fold change and q value.  

Now if the data is log2 transformed then numerator = "difference of means"
and the fold change should be = 2^(numerator). But this is not always true. For some genes it looks OK but for others the fold change calcuated by SAM is far different from that of 2^(numerator). So I think SAM considers a slightly different approach to estimate fold change. Do you know excatly how SAM estimates the fold change?  

Would really appreciate if you can help me with this.


Nikhil Garge
Research Programmer
Center for Biotech and Genomic Medicine
Medical College of Georgia
CA 4100, Augusta GA 30912

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