[BioC] plotHist and plotDeg?

[Lana Schaffer]

James,
> 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 am not able to use plotDeg() in R version2.5.0dev
and don't get a legend when using plotAffyRNAdeg() as I said earlier.

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]]
>>
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>
>
> -- 
> 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
>
>
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