[BioC] SAM output explanation and an FDR question

Ettinger, Nicholas nicholas-ettinger at uiowa.edu
Tue Jan 10 23:32:43 CET 2006

Hello all!

(A) For a not so statistically gifted grad student, can someone either
tell me or point me to a place where I can understand what exactly all
the columns in my "summary(sam.out)" data mean? I understand Delta,
cutlow, cutup and FDR but the others (s0, False, Called, j2, j1) I am
not exactly sure.  I looked through the siggenes vignette but this
question is not addressed specifically.

> summary(sam.out)

SAM Analysis for the One-Class Case  

 s0 = 0.1046  (The 30 % quantile of the s values.) 
 Number of permutations: 16 (complete permutation) 

 MEAN number of falsely called genes is computed.

   Delta    p0    False Called   FDR cutlow cutup    j2    j1
1    0.1 0.833 24511.25  27472 0.743 -0.130 1.459 26547 53751
2    0.2 0.833 2863.875   5314 0.449 -1.066   Inf  5314 54676
3    0.3 0.833  449.625   1085 0.345 -1.615   Inf  1085 54676
4    0.4 0.833       53    140 0.315 -2.307   Inf   140 54676

(B) A related question: is there any kind of consensus on "how much" FDR
is "too much" FDR?  In other words, it is pretty well accepted that for
small numbers of hypotheses, we want p <0.05 to guide us as to whether a
change is significant or not.  Has any kind of consensus evolved in a
similar manner for FDR?  Any primary literature addressing this?

Thank you!!

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