[BioC] why S-Score is not poppular like T-test pvalue and BH FDR , which is OK to use?

[Saurin Jani]

Hi Richard,

Thank you so much for the helpful information. S-Score
seems like very useful algorithm for microarray
analysis currently. I suppose, it will be very useful
when multivariate version comes out. 

Thank you again for your help and time,
S

--- Richard Kennedy <rkennedy at vcu.edu> wrote:

> Saurin,
> The S-Score is an algorithm for analyzing microarray
> data, originally
> developed in Michael Miles' laboratory at UCSF (by
> Li Zhang, currently
> at MD Anderson Cancer Center).  Dr. Miles has since
> relocated to our
> institution, and we are working as a group on the
> S-Score.
> 
> As Adaikalavan notes, the S-Score has not been
> heavily publicized, which
> may account in part for the lack of widespread use. 
> However, since the
> release of Dr. Miles' Journal of Neuroscience paper
> (Kerns et al, J
> Neurosci 2005, 25(9):2255-2266), we have been seeing
> increasing
> interest.  The S-Score does have some rather
> interesting features, with
> the main one being that it performs tests of
> hypotheses directly from
> the probe level data.  The usual steps in analysis
> require that a probe
> set summary measure be generated, and statistical
> tests are performed on
> the summaries.  Under conditions of no differential
> expression, the
> S-Scores follow a standard normal distribution; this
> means that
> hypothesis testing can be done directly with the
> S-Scores, without an
> intermediate expression summary measure.
> 
> There are, of course, some limitations with the
> S-Score as well.  The
> software had previously been available only as a
> compiled stand-alone
> program for Windows (at
> http:www.brainchip.vcu.edu/expressionda.html) so
> it took a few steps to combine it with an
> environment such as R.
> However, we have been working on an R implementation
> which, as Seth
> noted, should be posted in the near future.  This
> initial release is
> just a straight port of the Windows version to R; it
> does not add any
> new features, but does make it easier to interface
> with the other
> Bioconductor packages.  Another principal limitation
> of the S-Score is
> that the software performs comparisons two chips at
> a time.  We are now
> working on a multivariate version for direct
> multi-chip comparisons, but
> have not set a definite timeframe for its release.  
> 
> The main reference for the S-Score is Zhang et al, J
> Mol Biol 2002,
> 317:225-235 that describes some of the original
> development; Dr. Miles
> has also used the S-Score in several peer-reviewed
> publications.  We are
> in the process of submitting an article on
> additional validation studies
> of the S-Score (which did rather well compared to
> other methods) and an
> applications note for the R implementation.
> 
> Hope this has been helpful - we are definitely
> interested in making the
> S-Score more widely available.
> 
> Richard Kennedy
> Kellie J. Archer
> Department of Biostatistics
> Virginia Commonwealth University
> 
> 
> 
> Saurin Jani wrote:
> 
> >Dear BioC,
> >
> >Have any one used S-Score algorithm in order to
> >analyze microarray data and extracted diff.
> expressed
> >genes ? Or is it useful to use use...RMA ->  do
> t-test
> >get p-valule  -> and do FDR (BH) --> extract diff.
> >expressed genes?
> >
> >why S-score is not in much of use? like  T-test
> pvalue
> >and BH FDR..which is OK to use?  
> >
> >Thank you so much in advance,
> >S
> >
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>