[BioC] using mat.samp in siggenes

[Holger Schwender]

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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 

-- 
Supergünstige DSL-Tarife + WLAN-Router für 0,- EUR*
Jetzt zu GMX wechseln und sparen http://www.gmx.net/de/go/dsl