search for: marrayplots

...process, loads up some Bioconductor libraries, executes some R commands and takes the ouput and creates a web page. It is all very neat and works well. I am trying to make my cgi scripts quicker and it turns out that the bottle-neck is the loading of the libraries into R - for example loading up marrayPlots into R takes 10-20 seconds, which although not long, is long enough for users to imagine it is not working and start clicking reload.... So I just wondered if anyone had a neat solution whereby I could somehow have the required libraries permanently loaded into R - perhaps I need a persistent R pr...

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

...4 lables at the axis, it's enough to have one lable for all the different factor level combinations, which results in 28 labels. Maybe you have an idea how to setup the command to align the tick marks properly. thanks for your help, kind regards, Arne Here are my commands: > library(marrayPlots) # for the colors > col <- maPalette(low='white', high='darkred', k=50) > par(ps=8, cex=1, mar=c(1,5,5,1)) # space needed for lables @ axis 1 and 3 # x and y range from 1 to 84, x is the correlation matrix (dim = 84x84) > image(1:84, 1:84, x, col=col, xaxt='n',...

...QL, RmSQL, XML, rpvm, rsprng, RMpi, but not ROracle, RSQLite, RQuantlib -- Lindsay packages rmutil, gnlm, stable, growthm repeated, event, ordinal -- Bioconductor packages Biobase, annotate, affy, AnnBuilder, edd, genefilter, geneplotter, rhdf5, marrayTest, marrayClasses, marrayInput, marrayPlots, multtest, ROC, tkWidgets -- snow from Tierney -- deal from gR -- from Devel Dopt, GRASS, PHYLOGR, R2HTML, RPgSQL, dseplus, pls, runstat, multidim, mclust, ensemble, locfit, write-snns -- from OmegaHat gtk, OOP, RGtk, RGtkViewers, RObjectTables, RSPerl, RSPython what does NOT load tkrplot...

...- Improved interfaces (limmaGUI, affylmGUI, webbioc, -- MAGE file processing (RMAGEML) -- affymetrix processing: many improvements, gcrma, affypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packages) -- General analysis tools (rama, qvalue, pickgene, EBarrays, impute, pamr, bim, ) -- QA/QC (arrayMagic, arrayQuality, LPE) -- sequence analysis (pairseqsim, Biostrings) -- interface to the GeneSpring data analysis program (GeneSpring) TOOLS: ====== The released pac...

...sses, limma). * identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data (affy, affycomp, gcrma) * diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) * storage and retrieval of large datasets (rhdf5, externalVector, Rdbi, RdbiPgSQL). * facilitate user interaction (tkWidgets, widgetTools) There are currently a total of 48 packages, not including precomputed annotation data packages for Affymetrix GeneChips(tm), KEGG, GO, and LocusLink mapp...

...sses, limma). * identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data (affy, affycomp, gcrma) * diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) * storage and retrieval of large datasets (rhdf5, externalVector, Rdbi, RdbiPgSQL). * facilitate user interaction (tkWidgets, widgetTools) There are currently a total of 48 packages, not including precomputed annotation data packages for Affymetrix GeneChips(tm), KEGG, GO, and LocusLink mapp...