Thank you both. I now have it working! Best Wishes, Rachael Hageman ________________________________________ From: Wolfgang Huber [huber@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 >

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