[BioC] Siggenes/SAM vs Excel

Holger Schwender holger.schw at gmx.de
Fri Jul 4 05:04:30 CEST 2008

Hi Tom,

not sure how often I have answered this question here and in other forums. But okay once again: The defaults of siggenes and Excel SAM are a bit different:

- In siggenes, a moderated Welch's t-statistic is computed by default, whereas a moderated version of the ordinary t-statistic assuming equal group variances is used in Excel SAM. Set var.equal=TRUE in sam to use the ordinary t-statistic (only necessary if the sizes of the groups differ).

- In siggenes, the mean number of falsely called genes (warning: this is *not* the expected number of false positives) is computed, whereas the median number is used by Excel SAM. Set med=TRUE in sam to use the median number.

- In siggenes, a natural cubic spline based approach is used to estimate pi0, whereas Excel SAM uses an adhoc estimate. Set lambda=0.5 in sam to use this adhoc estimate.

- Even though I have implemented the computation of the fudge factor s0 exactly as described in the Excel SAM manual, the value of s0 usually differs between siggenes and Excel. Not sure why.

- In siggenes s0=0 is also a choice for the fudge factor. In the old version of Excel SAM it is not. Not sure about the new version.

- Have not found a description on how the q-values are estimated in Excel SAM. The values of the q-values usually differ between siggenes and Excel. In siggenes, the computation of the q-values is implemented in virtually the same way as in John Storey's R package qvalue such that q-values are typically the same. They only differ when there are tied p-values, since siggenes handles ties a bit different (in my opinion more correctly) than John's function qvalue.

- The same seed for the random number generator will not lead to the same permutations of the response.


-------- Original-Nachricht --------
> Datum: Thu, 3 Jul 2008 09:21:41 -0400
> Von: Thomas Hampton <Thomas.H.Hampton at Dartmouth.EDU>
> An: "Holger Schwender" <holger.schw at gmx.de>
> CC: bioc <bioconductor at stat.math.ethz.ch>
> Betreff: [BioC] Siggenes/SAM vs Excel

> How similar is  siggenes to the Stanford SAM with the Excel front end?
> Thanks!
> Tom 


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