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Question: SAM algorithm S0 value calculation
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gravatar for jaydeep chovatia
10.4 years ago by
jaydeep chovatia20 wrote:
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ADD COMMENTlink modified 10.4 years ago by James W. MacDonald45k • written 10.4 years ago by jaydeep chovatia20
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gravatar for James W. MacDonald
10.4 years ago by
United States
James W. MacDonald45k wrote:
Hi Jaydeep, jaydeep chovatia wrote: > Hi, > > > > I want to calculate S0 (exchangeability/fudge factor) value in Significance > Analysis of Microarray (SAM) algorithm. Is there any algorithm which > describes calculation of S0 value based on input data? Both the siggenes and samr packages calculate this parameter, so you should probably look there. Best, Jim > > > > Thank you, > > Jaydeep > > > DISCLAIMER\ ==========\ This e-mail may contain privileged a...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 10.4 years ago by James W. MacDonald45k
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gravatar for Stephen Henderson
10.4 years ago by
Stephen Henderson1.0k wrote:
In the original paper: "Significance analysis of microarrays applied to the ionizing radiation response". PNAS 2001 98: 5116-5121, (Apr 24). The calculation of s0 is described thus (page 2, first column): "The coefficient of variance of d(i) was computed as a function of s(i) in moving windows across the data. The value of s0 was chosen to minimize the coefficient of variance" s(i) is the measured standard deviation. d(i) is their relative difference score with s(i) + s0 in the denominator. Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of jaydeep chovatia Sent: 03 July 2007 10:37 To: bioconductor at stat.math.ethz.ch Cc: 'jaydeep chovatia' Subject: [BioC] SAM algorithm S0 value calculation Hi, I want to calculate S0 (exchangeability/fudge factor) value in Significance Analysis of Microarray (SAM) algorithm. Is there any algorithm which describes calculation of S0 value based on input data? Thank you, Jaydeep DISCLAIMER\ ==========\ This e-mail may contain privileged\ ...{{dropped}}
ADD COMMENTlink written 10.4 years ago by Stephen Henderson1.0k
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