Hi, I found a bug in the overview function from the made4 package. When I call overview with a marrayRaw object, I get the following error: > overview(RG.mRaw) Error in switch(class(arraydata), matrix = { : object "intensities" not found I traced this to the getdata function: }, marrayRaw = { if (require(affy, quiet = TRUE)) { nrslides = as.integer(ncol(arraydata at maRf)) nrspots = as.integer(nrow(arraydata at maRf)) tmp = matrix(NA, nrow = nrspots, ncol = 2 * nrslides) tmp[, (1:nrslides) * 2 - 1] = arraydata at maGf - intensities at maGb #perhaps intensities should be arraydata? tmp[, (1:nrslides) * 2] = arraydata at maRf - intensities at maRb #perhaps intensities should be arraydata? } as.data.frame(tmp) } When I replace 'intensities' with 'arraydata' in these two lines, it works just fine. Also, here's a suggested improvement - at least for 'marrayRaw' objects, sample names don't currently get used. I added the following to the getdata function to so the samples will be labeled: }, marrayRaw = { if (require(affy, quiet = TRUE)) { nrslides = as.integer(ncol(arraydata at maRf)) nrspots = as.integer(nrow(arraydata at maRf)) tmp = matrix(NA, nrow = nrspots, ncol = 2 * nrslides) tmp[, (1:nrslides) * 2 - 1] = arraydata at maGf - arraydata at maGb tmp[, (1:nrslides) * 2] = arraydata at maRf - arraydata at maRb tmp.names = vector(mode = "character", length = 2 * nrslides) tmp.names[(1:nrslides) * 2 - 1] = paste("G",colnames(arraydata at maGf),sep="_") tmp.names[(1:nrslides) * 2] = paste("R",colnames(arraydata at maRf),sep="_") colnames(tmp) = tmp.names } as.data.frame(tmp) } I'm enjoying the package, especially the html3D! Cheers, Jenny > sessionInfo() R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: affy convert marray Biobase made4 "1.8.1" "1.4.0" "1.8.0" "1.8.0" "1.4.0" scatterplot3d ade4 limma "0.3-24" "1.4-0" "2.4.4" > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 Ph: 217-244-7355 FAX: 217-265-5066 Email: drnevich at uiuc.edu

Hi Jenny, On 1 Dec 2005, drnevich at uiuc.edu wrote: > Hi, > > I found a bug in the overview function from the made4 package. When > I call overview with a marrayRaw object, I get the following error: [snip] Excellent bug report. I hope others on the list use this as an example :-) While I'm certain that *all* Bioc package maintainers read the bioconductor list, ;-) it is a very good idea to also send a mail directly to the package maintainer (as found in the package's DESCRIPTION file or via packageDescription("pkgname") in R). Best, + seth

Hi Jenny Thanks a million for your excellent bug report. It was very helpful. I will change the code today. I am very grateful for all bugs reports and comments on my package. Thanks a million Aedin > Message: 1 > Date: Fri, 02 Dec 2005 07:00:50 -0800 > From: Seth Falcon <sfalcon at="" fhcrc.org=""> > Subject: Re: [BioC] bug in overview function of made4 > To: bioconductor at stat.math.ethz.ch > Message-ID: <m2zmnj5ysd.fsf at="" ziti.local=""> > Content-Type: text/plain; charset=us-ascii > > Hi Jenny, > > On 1 Dec 2005, drnevich at uiuc.edu wrote: > > Hi, > > > > I found a bug in the overview function from the made4 package. When > > I call overview with a marrayRaw object, I get the following error: > [snip] > > Excellent bug report. I hope others on the list use this as an > example :-) > > While I'm certain that *all* Bioc package maintainers read the > bioconductor list, ;-) it is a very good idea to also send a mail > directly to the package maintainer (as found in the package's > DESCRIPTION file or via packageDescription("pkgname") in R). > > Best, > > + seth >