[BioC] plotHist and plotDeg?

[James W. MacDonald]

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
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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
>>
>>
>> **********************************************************
>> 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.