[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!!
---Nick
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