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

	[[alternative HTML version deleted]]


