[BioC] Interpreting the delta table from SAM

Holger Schwender holger.schw at gmx.de
Sat Jun 12 01:48:13 CEST 2010

Hi Casper,

these are the cutoffs for calling genes differentially expressing using the corrsponding delta value. Thus, for a given delta value all genes are called differentially expressed if their test score is larger than the cuthi value corresponding to the delta value or if their test score is smaller than cutlo.


-------- Original-Nachricht --------
> Datum: Fri, 11 Jun 2010 15:10:36 -0700
> Von: Casper Shyr <casshyr at hotmail.com>
> An: bioconductor at stat.math.ethz.ch
> Betreff: [BioC] Interpreting the delta table from SAM

> Dear all,   I performed a SAM (Significance Analysis for Microarray)
> analysis in R, and retrieved the delta table with the corresponding # of false
> positives, positives, FDR...etc for each delta. In that table, it also
> contains the columns "cutlo" and "cuthi". I can't find in the SAM manual what
> those two refer to, and what's their significance in terms of determining
> which delta value to use. Could someone help me on that?
> Thank you!Sincerely,Casper
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