PrintTip boxplots fail with the following error message under R 1.9.0 and Bioconductor v1.4: ?Error in boxplot.default(yy ~ xx, xlab = "PrintTip", ylab = "M", names = c("(1,1)", : names attribute [16] must be the same length as the vector [1]? The exact same test code works fine under R 1.8.1 (? and whatever version of Bioconductor I?m running there ?). library(marrayInput) swirl.layout <- read.marrayLayout(fname = "fish.gal", ngr = 4, ngc = 4, nsr = 22, nsc = 24, skip = 21,ctl.col = 4) ctl <- rep("Control", maNspots(swirl.layout)) ctl[maControls(swirl.layout) != "control"] <- "N" maControls(swirl.layout) <- factor(ctl) swirl.targets <- read.marrayInfo("SwirlSample.txt") swirl.gnames <- read.marrayInfo("fish.gal",info.id = 4:5, labels = 5, skip = 21) datadir <- getwd() fnames <- dir(path=datadir,pattern=paste("*", "spot", sep="\.")) swirl<- read.Spot(fnames, path=datadir, layout = swirl.layout, gnames = swirl.gnames, targets = swirl.targets) library(marrayPlots) maBoxplot(swirl[, 1]) Help would be appreciated. Thanks! Chuck Charles E. White, Senior Biostatistician, M.S. Walter Reed Army Institute of Research 503 Robert Grant Ave., Room 1w102 Silver Spring, MD 20910-1557 301 319-9781 Personal/Professional Site: http://users.starpower.net/cwhite571/professional/

> library(marrayInput) > library(marrayPlots) Both of these commands will throw a warning. The text of that warning should give you a hint as to what the problem is :) For example: Warning message: marrayInput is a deprecated package. Please use the marray package instead. in: firstlib(which.lib.loc, package)

Hi Charles, Please use the combined package "marray". Try library(marray) data(swirl) boxplot(swirl[,1]) cheers Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Lung Biology Center, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> (1) The default packages downloaded by BioC() do not include "marray" You should be getting 'marray' by default. It is part of the 'cdna' bundle in getBioC which is itself part of the default. > (2) Default packages DO include "marrayInput" & "marrayPlots" Right, there were a couple of package maintainers who did not update their dependencies properly. The marrayInput and marrayPlots packages are not directly being downloaded and installed but gotten as part of the dependency checking for these other packages. > (3) The warning messages I get without downloading "marray" are as follows: > > library(marrayInput) > Loading required package: marrayClasses > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > > library(marrayPlots) > Warning message: > package 'modreg' has been merged into 'stats' Wait, are you downloading release 1.4 packages or 1.3 packages?

> >From the 1.4 web page, I pulled down and executed getBioC version 1.2.58 > yesterday before I executed my test code and provided you with the messages > I obtained. I guess I'm going to have to break this habit, but I still > determine whether a package is available by looking at the package list > under HTML help. I didn't see marray on that page until I explicitly > downloaded it using the R GUI. I'm fairly certain that marrayy is indeed getting downloaded by the default getBioC (and in fact only 'marray' and not any of thee old 'marrayXYZZ' packages - I know though that this wasn't the case a few days ago, so it might have only been true when you first did this) as this is what just happened here (and also what is specified by the default setting). That being said - there does seem to be something weird with the HTML help not being updated after getBioC(), I installed one package from "Install Packages from Bioconductor" and then everything I downloaded via getBioC is now on the HTML Help. I'll take aa look at this. -J