[BioC] Doubt regarding 'playerout' and 'medianpolish' in affy package

[Laurent Gautier]

On Tue, Feb 04, 2003 at 09:49:32AM -0800, Tapan Mehta wrote:
> Hello,
> 
> Thank you both of you  for your help. I really
> appreciate it. 
> 
> However the information provided by the help does not
> seem to be sufficient. I does not seem to explain the
> logic/purpose of the options. Please can I get more
> guidance about it. This is what I get when I type the
> command:
> 
> >help.search("playerout")
> 
> Help files with alias or title matching `playerout',
> type 'help(FOO, package = PKG)' to inspect entry
> 'FOO(PKG) TITLE':
> 
> generateExprVal.method.playerout(affy)
>                                      Generate an
> expression value from the probes informations
> 
> 
> Please let me know if there is any way to trace the
> logic in the various options.


A very powerful feature of R (and S/S-plus) is the help system.
All you need is to call the function 'help'. For example
'help(help)' will query help about the function help. If you are
begining with R, you may find a call to 'help.start()' handy too.
You may want read more about all that in a book/manual about R/S-plus.

...but in the meanwhile, try:
help(generateExprVal.method.playerout, package=affy)


Hopin' it helps,

L.


> 
> Thanking you,
> 
> Tapan Mehta 
> --- Laurent Gautier <laurent@cbs.dtu.dk> wrote:
> > On Mon, Feb 03, 2003 at 08:36:17PM -0800, Tapan
> > Mehta wrote:
> > > Hello,
> > > 
> > > I am  currently using the affy package of
> > > Bioconductor. It would be great if somebody could
> > > provide some information about the 'playerout'
> > option
> > > in the summary.method that can be used in the
> > expresso
> > > function.  
> > 
> > The names of the functions are not very short, but
> > they can be
> > easily found using the following incantation:
> > 
> > help.search("playerout")
> > help.search("medianpolish")
> > 
> > 
> > 
> > Hopin' it helps,
> > 
> > 
> > 
> > L.
> > 
> > 
> > > 
> > > I also encountered a similar doubt regarding the
> > > medianpolish option which I think to be a Tukey's
> > > biweight procedure. Please guide me about the
> > same.
> > > Also, is there a way/documentation by which  one
> > can
> > > understand the logic behind various options ?
> > > 
> > > Thanking you,
> > > 
> > > Regards
> > > 
> > > Tapan Mehta
> > > 
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > >
> >
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > 
> > -- 
> >
> --------------------------------------------------------------
> > currently at the National Yang-Ming University in
> > Taipei, Taiwan
> >
> --------------------------------------------------------------
> > Laurent Gautier			CBS, Building 208, DTU
> > PhD. Student			DK-2800 Lyngby,Denmark	
> > tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> >
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> 
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-- 
--------------------------------------------------------------
currently at the National Yang-Ming University in Taipei, Taiwan
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent