[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.

Thanks,
~Nikhil.  

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

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