search for: cdna

...with the RDF package to download data from a website, and then use R to manipulate it. Text on the website is UTF-8. The RDF package's rdf_load command is converting it into a different encoding, which converts non-ASCII characters to unicode codes. On the webpage/sparql RDF: "4.5µg of cDNA was used" In R, the RDF triple gives: "4.5\\u00B5g of cDNA was used" I can't seem to convert it back from \\u00B5 into "µ". I've tried iconv with various settings without success: > iconv(test, "latin1", "UTF-8") [1] "4.5\\u00B5g of c...

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

...--max-mem-size=2G but I run out of memory somewhere around 500Mb (which is why I am trying to find out how much memory is allocated). I don't have any other programs open, so I should certainly be able to address more memory than that. Any ideas? TIA 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

Hello, I'm a french student working on a project concerning cDNA microarray. I've chosen to work with R and use the marrayClasses, marrayInput (...) packages. First, when I enter "library(marrayInput)", R warns me about a missing package called "utils" but I can't find it anywhere. Normally this package is installed when you install...

...draw a deep-blue Affymetrix image through Image() function in Affy package? The default settings of image() draw me a black-white image and if I modify it to 256 colors, I get a somehow yellowish image. The reason for me to draw a deep-blue one is because I found most of papers display the spotted cDNA microarray image as red-green and the Affymetrix chip image as deep-blue. Thank you very much, Frank [[alternative HTML version deleted]]

hi,everybody I have a *time course* data set about a CML cell line treated by two drugs and their combination.The experiment was performed on cDNA microarray platform.The green channel of all the arrays are common,the untreated cell.Here follows the experiment design: a_0hr,a_3hr,a_8hr,a_12hr,a_24hr,a_48hr,a_72hr, b_3hr,b_8hr,b_12hr,b_24hr,b_48hr,b_72hr, ab_3hr,ab_8hr,ab_12hr,ab_24hr,ab_48hr,ab_72hr. A total of 19 *cDNA microarrays*.a_0...

..." $system [1] "i386, mingw32" $status [1] "Under development (unstable)" $major [1] "2" $minor [1] "1.0" $year [1] "2005" $month [1] "03" $day [1] "17" $language [1] "R" 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

...ve() and texi2dvi() are run. Unfortunately, the above code chunks no longer work. I can certainly hard code the first chunk to find the .Rdata file, but I have to imagine there is a much more elegant way to do this. Any suggestions? Best, Jim -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

...day 29 svn rev 37607 language R version.string Version 2.3.0 alpha (2006-03-29 r37607) Best, Jim James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

...mingw32 status = major = 1 minor = 9.0 year = 2004 month = 04 day = 12 language = R Windows XP Professional (build 2600) Service Pack 1.0 Search Path: .GlobalEnv, package:methods, package:stats, package:graphics, package:utils, Autoloads, package:base 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

I've tried looking at ?colors and ?palette and if I'm understanding it correctly, I'm supposed to type in (for example) palette(rainbow(13)) before I type in my plot (of 13 lines) if I want 13 different colors. But this does not work. Other things that i have tried besides rainbow give me errors. Am I just doing something completely wrong? Anna

...t even if all I have in my .GlobalEnv are functions. A trivial example is to run the examples from the package.skeleton() help page. I believe there should be two data type and two function type .Rd files, but instead they are all of the data type. Best, 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

...l ApoAI-/- k3 a1kok3.spot Pool ApoAI-/- k4 a1kok4.spot Pool ApoAI-/- k5 a1kok5.spot Pool ApoAI-/- k6 a1kok6.spot Pool ApoAI-/- k7 a1kok7.spot Pool ApoAI-/- k8 a1kok8.spot Pool ApoAI-/- > spottypes=readSpotTypes("ApoAISpotTypes.txt") > spottypes SpotType ID Name Color 1 cDNA * * black 2 BLANK BLANK * brown 3 Blank Blank * orange 4 Control Control * blue > RG$genes$Status=controlStatus(spottypes, RG) Matching patterns for: Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, : attempt to set an attribu...

Hi Everyone, I have been trying to read some Arrayvision files( 2 channel cDNA) and am having some problem. My code is : setwd('C:/work/data/limma/ndd1'); files <- c('ndd1_1.txt','ndd1_2.txt','ndd1_3.txt'); RG=read.maimages(files,"arrayvision",sep="\t"); #Normalisation MA=normalizeWithinArrays(RG); #plotPrintTipLoess(...

Greetings, I have "inherited" a cDNA macroarray dataset that is structured as follows. Three different stressors were tested. For each stressor, there are two treatments (control and stressed). For each treatment, two biological replicates exist, and these are paired (i.e., there is a stressed array for colony A and a control array...

Is it possible to use R as a data-mining tool? Here's the problem I've got. I have a couple of data sets consisting of results from a cDNA microarray experiment - the details about the biology don't really matter here, the same theory applies for any other data-mining task (that's why I thought it'd be more appropriate to post this on r-user). Each of these datasets consists of about 30000 rows by 20 to 30 columns. Let...

...day 10 svn rev 39242 language R version.string R version 2.4.0 alpha (2006-09-10 r39242) TIA, Jim James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

...svn rev 36947 language R version.string Version 2.3.0 Under development (unstable) (2006-01-01 r36947) 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

...Under development (unstable) (2008-02-18 r44516) i386-apple-darwin8.11.1 locale: C attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] tcltk_2.7.0 tools_2.7.0 -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

...lation and Management - Graphics; Enhancing Plots, Trellis - Writing Functions - Connecting to External Software - R/S Packages and Libraries (e.g. BioConductor) - BioConductor: Overview; Installation and Demonstration - Array Quality Inspection - Correction and Normalization; Affymetrix and cDNA arrays - Identification of Differentially Expressed Genes - Visualization of Genomic Information - Clustering Methods in R/Splus - Gene Ontology (GO) and Pathway Analysis - Inference, Strategies for Large Data (2) R/Splus Fundamentals and Programming Techniques Cour...