[BioC] ExpressionSet, fitPLM confusion

[Henrik Bengtsson]

Hi,

maybe a workaround would be to have a copy of the new version of
.Deprecated() in the global environment.  Here it is:

.Deprecated <- function (new, package = NULL, msg) {
  if (missing(msg)) {
    msg <- gettextf("'%s' is deprecated.\n",
as.character(sys.call(sys.parent())[[1]]))
    if (!missing(new))
       msg <- c(msg, gettextf("Use '%s' instead.\n", new))
    msg <- c(msg, if (!is.null(package)) gettextf("See
help(\"Deprecated\") and help(\"%s-deprecated\").", package) else
gettext("See help(\"Deprecated\")"))
  } else msg = as.character(msg)
    warning(paste(msg, collapse = ""), call. = FALSE, domain = NA)
}

If you don't bother with the 'msg' you could even do:

.Deprecated <- function(..., msg) base::.Deprecated(...)

I haven't tried it with your example, though.

/Henrik

On 12/15/06, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> Hi Georg,
>
> In addition to what Wolfgang told you, the affyPLM package in the devel
> repository won't work with R-2.5.0 yet, because some of the changes that
> have been made to the ExpressionSet object have not been addressed in
> the affyPLM package.
>
>  > dat <- ReadAffy()
>  > pset <- fitPLM(dat)
> Error in checkSlotAssignment(object, name, value) :
>         assignment of an object of class "AnnotatedDataFrame" is not valid for
> slot "phenoData" in an object of class "PLMset"; is(value, "phenoData")
> is not TRUE
> In addition: Warning message:
> The exprSet class is deprecated, use ExpressionSet instead
>
> Your best bet at this time is to go back to using release versions.
>
> Best,
>
> Jim
>
>
> Wolfgang Huber wrote:
> >
> > Dear Georg,
> >
> > to use the devel versions of Bioconductor (ie what will be Bioconductor
> > 2.0) you will need to use a more recent version of R (what will be R
> > 2.5): the new code in Biobase uses an argument "msg" of the .Deprecated
> > function that was not yet there in R 2.4.
> >
> > See http://www.bioconductor.org/download/BioC2.0/
> > "BioC 2.0 is currently in development. It is being designed to work with
> > R 2.5.z and is expected to be released in April of 2007."
> >
> >  Best wishes
> >  Wolfgang
> >
> >  Otto wrote:
> >
> >>Dear Bioconductors,
> >>
> >>Once more, I am a bit confused about an error linked with the new
> >>ExpressionSet class. What I am trying to do is to apply fitPLM to an
> >>AffyBatch object. First, I generate the AffyBatch object like this:
> >>
> >>targets<-new("AnnotatedDataFrame")
> >>pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2)
> >>
> >>
> >>Data<-ReadAffy(celfile.path =cel.path,
> >>               filenames = sampleNames(targets),
> >>               verbose=TRUE)
> >>
> >>
> >>Then I use fitPLM and get an error:
> >>
> >>Pset<-fitPLM(Data)
> >>
> >>Error in .Deprecated(msg = EXPRSET_DEPR_MSG) :
> >>      unused argument(s) (msg = "The exprSet class is deprecated, use ExpressionSet instead")
> >>
> >>However ?fitPLM tells me:
> >>
> >>This function converts an 'AffyBatch' into an 'PLMset' by fitting a
> >>specified robust linear model to the probe level data
> >>
> >>And class() confirms that my object is indeed an AffyBatch:
> >>
> >>class(Data)
> >>[1] "AffyBatch"
> >>attr(,"package")
> >>[1] "affy"
> >>
> >>
> >>I think I am working with the last versions of the needed libraries
> >>(see below). They were updated from the devel repository from
> >>source. Any hints?
> >>
> >>Best,
> >>
> >>Georg
> >>
> >>
> >>sessionInfo()
> >>
> >>R version 2.4.0 (2006-10-03)
> >>x86_64-redhat-linux-gnu
> >>
> >>locale:
> >>LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >>
> >>attached base packages:
> >>[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
> >>[7] "datasets"  "methods"   "base"
> >>
> >>other attached packages:
> >>zebrafishcdf      affyPLM        gcrma  matchprobes     affydata         affy
> >>    "1.15.0"     "1.11.8"      "2.7.1"      "1.7.1"     "1.11.1"    "1.13.12"
> >>      affyio      Biobase
> >>     "1.3.1"    "1.13.28"
> >>
> >>_______________________________________________
> >>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
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
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