Lana Schaffer wrote: > I am not able to use plotDeg() in R version2.5.0dev > and don't get a legend when using plotAffyRNAdeg() as I said earlier. plotAffyRNAdeg() doesn't make a legend, and you need to load affycoretools in order to use plotDeg(), which does (the same holds true for plotHist() which is in affycoretools as well). Best, Jim > > R version 2.5.0 Under development (unstable) (2007-01-06 r40395) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > affydata simpleaffy hgu133plus2cdf biomaRt RCurl > "1.11.1" "2.9.1" "1.14.0" "1.9.18" "0.8-0" > XML GOstats Category genefilter survival > "1.4-1" "2.1.9" "2.1.8" "1.13.7" "2.30" > KEGG RBGL annotate GO graph > "1.15.1" "1.11.3" "1.13.3" "1.15.1" "1.13.2" > limma affy affyio Biobase > "2.9.8" "1.13.12" "1.3.1" "1.13.30" > > ----- Original Message ----- From: "James W. MacDonald" > <jmacdon at="" med.umich.edu=""> > To: "Lana Schaffer" <schaffer at="" scripps.edu=""> > Cc: <bioconductor at="" stat.math.ethz.ch=""> > Sent: Wednesday, March 14, 2007 10:22 AM > Subject: Re: [BioC] plotHist and plotDeg? > > >> Hi Lana, >> >> Lana Schaffer wrote: >> >>> James, >>> When I use R version 2.4.0 (2006-10-03) I am able to >>> use plotHist() and plotDeg(() on my Affy chips and get a legend >>> telling me which chips correspond to each curves. However, when >>> I use R version 2.5.0 Under development I have produced the >>> "Error: could not find function "plotHist" or "plotDeg". When I used >>> plotAffyRNAdeg() >>> all the lines are the same color and there is no legend to distinguish >>> the curves. There is no "plotHist" in version 2.5dev and >>> "plotDensity" is not >>> looking the same as "plotHist". >>> I am wondering what your intentions are for these functions in R >>> version 2.5dev? >> >> >> The only change that I remember to these functions is that I now put >> the legend for plotDeg() outside the plotting area so it doesn't >> obscure the plotted lines. I use these functions on a nearly daily >> basis, and haven't had any problems. Can you give me the output to >> sessionInfo()? >> >> Best, >> >> Jim >> >> >>> >>> Lana Schaffer >>> Biostatistics/Informatics >>> The Scripps Research Institute >>> DNA Array Core Facility >>> La Jolla, CA 92037 >>> (858) 784-2263 >>> (858) 784-2994 >>> schaffer at scripps.edu >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >> >> >> >> -- >> 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. >> >> > -- 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.