[BioC] missing functions in affy package

[laurent]

On Mon, 2008-11-03 at 21:55 +0000, Wolfgang Huber wrote:
> Hi Rachel,
> 
> I suspect that you were using the "normalize.quantiles"  function from the
> "preprocessCore" package. When affy did not have a namespace, that package
> would automatically be attached whenever you said: library("affy"). Now,
> it is then only loaded but not attached.

Trickier than that, I would say.

"normalize.quantiles" used to be in "affy", then moved to
"preprocessCore" (but the absence of namespace made it hard to notice).

May be a dummy function left in affy (calling ".Deprecated") would make
sense ?


L.


> The easiest solution for you is probably:
> 
> > library("preprocessCore")
> > normalize.quantiles
> function (x, copy = TRUE)
> {
>     rows <- dim(x)[1]
>     cols <- dim(x)[2]
>     if (!is.matrix(x)) {
>         stop("Matrix expected in normalize.quantiles")
>     }
>     if (is.integer(x)) {
>         x <- matrix(as.double(x), rows, cols)
>         copy <- FALSE
>     }
>     .Call("R_qnorm_c_handleNA", x, copy, PACKAGE = "preprocessCore")
> }
> <environment: namespace:preprocessCore>
> 
> 
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] preprocessCore_1.4.0
> 
> 
> 
> 
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Http:  www.ebi.ac.uk/huber
> -------------------------------------
> 
> 
> 
> <quote who="James W. MacDonald">
> > Hi Rachael,
> >
> > The affy package now has a namespace, and I am sure this isn't an
> > exported function. If you want to use it directly, you can get to it
> > using the ':::' operator (e.g., affy:::normalize.quantiles()).
> >
> > Best,
> >
> > Jim
> >
> >
> >
> > Rachael Hageman wrote:
> >> To Whom it May Concern,
> >>
> >> I use the function "normalize.quantiles" in the preprocessCore/affy
> >> package on a regular basis for my illumina data.  I have recently
> >> installed the latest version of R (2.8) and the affy package off of
> >> Bioconductor.  I noticed that this function no longer exists within
> >> the package.  I wonder if this is an oversight on my part, or if it
> >> isn't, is there is a reason it was pulled from the package?  I am on
> >> a Mac, although my Windows machine has the same problem with the new
> >> version.
> >>
> >> Thanks in advance, Rachael
> >>
> >> _______________________________________________ Bioconductor mailing
> >> list Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
> >> archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > Hildebrandt Lab
> > 8220D MSRB III
> > 1150 W. Medical Center Drive
> > Ann Arbor MI 48109-0646
> > 734-936-8662
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor