To the Bioconductor Community Dear All, Firstly I would like to thank you all for the excellent advice that you have given me as I process my single-colour Agilent data using the R package "Agi4x44PreProcess". I am trying to build the expression set, and would like to plot a heatmap showing the 100 greater variance genes. The first time I ran the function: esetPROC = build.eset(ddPROC, targets, makePLOT = TRUE, annotation.package = "notAnnPack"), R returned: Error in HeatMap(exprs(esetPROC), size, maintitle) : could not find function "maPalette" I googled and found that maPalette is a feature of marray, and so I installed the most recent version of marray. Now when I run the same command (having also loaded the library "marray"), I get the error: Error in HeatMap(exprs(esetPROC), size, maintitle) : could not find function "heatmap.2" I have tried searching for advice on this but can only find help on how to alter the output of the heatmap, rather than the commands. Have I confused the software by loading the "marray" package? Should I have installed additional packages to plot the heatmap, or is this a general bug? FYI, my version of R is R 2.10.1 Many thanks in anticipation of your help. With Very Best Wishes Samantha (Sam) England Department of Physiology, Development & Neuroscience Anatomy Building Downing Street Cambridge, CB2 3DY UK

Hi Samantha, heatmap.2 is found in the "gplots" package, so try installing/loading that. Regards, Pete On Tue, Jul 27, 2010 at 4:56 AM, Samantha England <sje28@cam.ac.uk> wrote: > To the Bioconductor Community > > Dear All, > > Firstly I would like to thank you all for the excellent advice that you > have given me as I process my single-colour Agilent data using the R package > "Agi4x44PreProcess". > > I am trying to build the expression set, and would like to plot a heatmap > showing the 100 greater variance genes. The first time I ran the function: > > esetPROC = build.eset(ddPROC, targets, makePLOT = TRUE, annotation.package > = "notAnnPack"), R returned: > > Error in HeatMap(exprs(esetPROC), size, maintitle) : > could not find function "maPalette" > > I googled and found that maPalette is a feature of marray, and so I > installed the most recent version of marray. Now when I run the same > command (having also loaded the library "marray"), I get the error: > > Error in HeatMap(exprs(esetPROC), size, maintitle) : > could not find function "heatmap.2" > > I have tried searching for advice on this but can only find help on how to > alter the output of the heatmap, rather than the commands. Have I confused > the software by loading the "marray" package? Should I have installed > additional packages to plot the heatmap, or is this a general bug? FYI, my > version of R is R 2.10.1 > > Many thanks in anticipation of your help. > > With Very Best Wishes > > Samantha (Sam) England > > Department of Physiology, Development & Neuroscience > Anatomy Building > Downing Street > Cambridge, CB2 3DY > UK > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Samantha, try the command sessionInfo() and check wether the "gplots" package is loaded. If not, then load it our self. This package should contain the heatmap.2. cheers Benjamin Am 27.07.2010 um 10:56 schrieb Samantha England: > To the Bioconductor Community > > Dear All, > > Firstly I would like to thank you all for the excellent advice that you have given me as I process my single-colour Agilent data using the R package "Agi4x44PreProcess". > > I am trying to build the expression set, and would like to plot a heatmap showing the 100 greater variance genes. The first time I ran the function: > > esetPROC = build.eset(ddPROC, targets, makePLOT = TRUE, annotation.package = "notAnnPack"), R returned: > > Error in HeatMap(exprs(esetPROC), size, maintitle) : > could not find function "maPalette" > > I googled and found that maPalette is a feature of marray, and so I installed the most recent version of marray. Now when I run the same command (having also loaded the library "marray"), I get the error: > > Error in HeatMap(exprs(esetPROC), size, maintitle) : > could not find function "heatmap.2" > > I have tried searching for advice on this but can only find help on how to alter the output of the heatmap, rather than the commands. Have I confused the software by loading the "marray" package? Should I have installed additional packages to plot the heatmap, or is this a general bug? FYI, my version of R is R 2.10.1 > > Many thanks in anticipation of your help. > > With Very Best Wishes > > Samantha (Sam) England > > Department of Physiology, Development & Neuroscience > Anatomy Building > Downing Street > Cambridge, CB2 3DY > UK > _______________________________________________ > 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 > ___________________________________________ Benjamin Otto, PhD University Medical Center Hamburg-Eppendorf Institute For Clinical Chemistry / Central Laboratories Campus Forschung N27 Martinistr. 52, D-20246 Hamburg Tel.: +49 40 7410 51908 Fax.: +49 40 7410 54971 ___________________________________________ -- Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit?tsklinikum Hamburg-Eppendorf K?rperschaft des ?ffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. J?rg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Joachim Pr?l? Prof. Dr. Dr. Uwe Koch-Gromus