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
>
>
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--
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
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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}}
