[BioC] using mat.samp in siggenes

[Kathleen Kerr]

Thanks very much for this extended reply.
Out of curiosity, does sam() do unbalanced
permutations when the data are paired?  If so,
I suggest that it should default to only
doing balanced permutations.  By 'balanced'
in the paired case, I mean that within each pair
the assignment to treatment/control is randomized.
Actually, I'm not sure what 'balanced' means in the context
of unpaired data.

Thanks again,
Katie

----- Original Message ----- 
From: "Holger Schwender" <holger.schw at gmx.de>
To: "James W. MacDonald" <jmacdon at med.umich.edu>
Cc: <katiek at u.washington.edu>; <bioconductor at stat.math.ethz.ch>
Sent: Thursday, September 16, 2004 2:28 AM
Subject: Re: [BioC] using mat.samp in siggenes


> In the next version of siggenes, version 1.2.x, which will (hopefully) be
> part of Release 1.5 of Bioconductor, it won't be necessary anymore (for a
> SAM analysis) to specify mat.samp if you wanna do complete permutation
since
> this will be possible by setting B=0 or to an integer equal to or larger
> than the number of all possible permutations. However, it is still
possible
> to specify mat.samp if you, e.g., would like to use only balanced
> permutations.
>
> Besides from this, there will be many more changes in siggenes since I
have
> rewritten the code for a SAM analysis. E.g., the function sam.plot is
> replaced by the functions plot and summary, 'data' in sam(...) can be also
> an exprSet object (using an exprSet object, pData can be used for
specifying
> cl), it is possible to do a two class unpaired analysis assuming *unequal*
> variances, i.e. an analysis using Welch's t-statistic, a multiclass
analysis
> or an analysis of categorical data such as SNP data, respectively, it is
> possible to add the locus links to the output, the significant genes are
now
> ordered by their absolute value, i.e. by their "significance", ...
>
> The usage of sam will, however, be almost the same -- at least for the
> "important" arguments. I have only changed the default of med to med=FALSE

> which means that the mean (and not the median) number of falsely called
> genes is computed by default.
>
> There also will be a manual (hopefully a vignette) which will describe all
> these changes. Thanks to Kathleen, I will also add a section of how
mat.samp
> has to be specified. I have almost forgotten this.
>
> There however will be *no* changes in the empirical Bayes functions. New
> versions of find.a0, ebam and ebam.wilc with the same features as sam
might
> possibly be part of Release 1.6 of Bioconductor.
>
> Sorry for this pretty long mail. I actually only wanted to say that
complete
> permutation is possible in the next version of siggenes.
>
> Best,
> Holger
>
>
>
> > Kathleen Kerr wrote:
> >
> > > I am using the sam() function in siggenes and I
> > > cannot find information about using the option mat.samp:
> > >
> > >  mat.samp: a permutation matrix. If specified, this matrix will be
used,
> > >         even if 'rand' and 'B' are specified.
> > >
> > > I have a dataset with four treated samples and four control samples
> > > that are paired, so my class label is:
> > > cl=c(-1,-2,-3,-4, 1,2,3,4)
> > >
> > > There are only 2^4=16 permutations, so I would just like to enumerate
> > > them.  The helpfile doesn't give any information about what the
> > > permutation matrix should look like.
> >
> > The permutation matrix should be a 16 x 4 matrix of 1's and -1's
> >
> > 1 1 1 1
> > -1 1 1 1
> > 1 -1 1 1
> > 1 1 -1 1
> > etc
> >
> > HTH,
> >
> > Jim
> >
> >
> >
> > >
> > > I have tried the matrix with sixteen rows, each of which
> > > looks something like
> > > c(-1, 2, 3,-4, 1,-2,-3,4)
> > > but I get an error message that this is invalid.
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> >
> > -- 
> > James W. MacDonald
> > Affymetrix and cDNA Microarray Core
> > University of Michigan Cancer Center
> > 1500 E. Medical Center Drive
> > 7410 CCGC
> > Ann Arbor MI 48109
> >
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> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
>
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