[BioC] missing functions in affy package

[Rachael Hageman]

Thank you both.
I now have it working!
Best Wishes,
Rachael Hageman
________________________________________
From: Wolfgang Huber [huber at ebi.ac.uk]
Sent: Monday, November 03, 2008 4:55 PM
To: James W. MacDonald
Cc: Rachael Hageman; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] missing functions in affy package

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.

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
>