Dear all, I would be grateful if someone could help me with a small thing I am stumbl= ing over and can not solve: When trying to plot AffyBatch (totally 8 experiments in this case) using hi= st() and plotAffyRNAdeg() I can only plot multiple slides (e.g using [1:2])= but I am not able to plot just one chip. (I want to be able to tell differ= ent curves apart).=20 I have tried [1] and [1:1] but get the same error message: > library(affy) > NHEK<- ReadAffy(widget=3DTRUE) > hist(NHEK[1]) Error in apply(mat, 2, density) : dim(X) must have a positive length I am working on windows with Rw1071 and updated all my packages from CRAN a= nd Bioconductor yesterday from within the program. All the best! :o) // Anna ********************************************************************** *****= **************** Anna Gustafsson Royal Institute of Technology AlbaNova University Center Stockholm Center for Physics, Astronomy and Biotechnology Department of Molecular Biotechnology 106 91 Stockholm, Sweden Phone (office): +46 8 553 783 41 Fax: + 46 8 553 784 81 Visiting adress: Roslagstullsbacken 21, Floor 3 Delivery adress: Roslagsv=E4gen 30B ********************************************************************** *****= ****************=20 [[alternative HTML version deleted]]

If you are just trying to tell the curves apart, you might simply give them different colors. I usually use something like this: hist(NHEK, type="l", lty=1, lwd=2, col=1:8) followed by legend(12, 0.25, legend=filenames, lty=1, lwd=2, col=1:8) for the RNA deg: plotAffyRNAdeg(AffyRNAdeg(NHEK), col=1:8)) HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Anna Gustafsson <annag@biotech.kth.se> 08/13/03 09:34AM >>> Dear all, I would be grateful if someone could help me with a small thing I am stumbling over and can not solve: When trying to plot AffyBatch (totally 8 experiments in this case) using hist() and plotAffyRNAdeg() I can only plot multiple slides (e.g using [1:2]) but I am not able to plot just one chip. (I want to be able to tell different curves apart). I have tried [1] and [1:1] but get the same error message: > library(affy) > NHEK<- ReadAffy(widget=TRUE) > hist(NHEK[1]) Error in apply(mat, 2, density) : dim(X) must have a positive length I am working on windows with Rw1071 and updated all my packages from CRAN and Bioconductor yesterday from within the program. All the best! :o) // Anna ********************************************************************** ********************* Anna Gustafsson Royal Institute of Technology AlbaNova University Center Stockholm Center for Physics, Astronomy and Biotechnology Department of Molecular Biotechnology 106 91 Stockholm, Sweden Phone (office): +46 8 553 783 41 Fax: + 46 8 553 784 81 Visiting adress: Roslagstullsbacken 21, Floor 3 Delivery adress: Roslagsv?gen 30B ********************************************************************** ********************* [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

this is a bug. the line x <- intensity(x)[Index, ] in the function plotDensity.AffyBatch should be x <- intensity(x)[Index, ,drop=FALSE] while we fix it for the next release, you can change it or simply call plotDensity(exprs(NHEK[1])) -r apply(mat, 2, density) On Wed, 13 Aug 2003, Anna Gustafsson wrote: > Dear all, > > I would be grateful if someone could help me with a small thing I am stumbling over and can not solve: > > When trying to plot AffyBatch (totally 8 experiments in this case) using hist() and plotAffyRNAdeg() I can only plot multiple slides (e.g using [1:2]) but I am not able to plot just one chip. (I want to be able to tell different curves apart). > I have tried [1] and [1:1] but get the same error message: > > > library(affy) > > NHEK<- ReadAffy(widget=TRUE) > > hist(NHEK[1]) > Error in apply(mat, 2, density) : dim(X) must have a positive length > > I am working on windows with Rw1071 and updated all my packages from CRAN and Bioconductor yesterday from within the program. > > All the best! :o) > // Anna > > > ******************************************************************** *********************** > Anna Gustafsson > > Royal Institute of Technology > AlbaNova University Center > Stockholm Center for Physics, Astronomy and Biotechnology > Department of Molecular Biotechnology > 106 91 Stockholm, Sweden > > Phone (office): +46 8 553 783 41 > Fax: + 46 8 553 784 81 > Visiting adress: Roslagstullsbacken 21, Floor 3 > Delivery adress: Roslagsv?gen 30B > ******************************************************************** *********************** > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >