[BioC] plotDeg in affycoretools

[James W. MacDonald]

Hi Claire,

The affystart() function should have dumped pdfs for all three plots in 
your working directory. Let me know if they are not there.

I wrote affystart() for those situations where I am not doing the 
analysis. I just wanted to do some quick QA plots and compute expression 
values that I can send on to whomever is actually doing the work. So 
really, this is not the function you want for an interactive analysis.

Instead something like this would work.

dat <- ReadAffy()
plotHist(dat)
plotDeg(dat)
eset <- rma(dat)
plotPCA(eset)
..


You might also take a look at the affyQCReport package, which will do 
some other QA stuff as well.

Best,

Jim

claire wilson wrote:
> Hi Jim,
> 
> Many thanks for your prompt reply. I have used the affystart function to
> load the data into R. How do I access the raw data and not just the
> expression set. I would like to see the degradation and density plots,
> but only the PCA one remained.
> 
> Kind Regards
> 
> Claire 
> 
> 
>>-----Original Message-----
>>From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
>>Sent: 22 March 2007 13:53
>>To: claire wilson
>>Cc: bioconductor at stat.math.ethz.ch
>>Subject: Re: [BioC] plotDeg in affycoretools
>>
>>Hi Claire,
>>
>>claire wilson wrote:
>>
>>>Hi all,
>>> 
>>>am getting the following error when I call plotDeg from 
>>
>>affycoretools, 
>>
>>>can anyone help me out?
>>
>>It would appear that you are calling plotDeg() on an exprSet, 
>>rather than an AffyBatch. At the exprSet stage you have 
>>already computed expression values, so there are no longer 
>>any pm probes to plot.
>>
>>Best,
>>
>>Jim
>>
>>
>>
>>> 
>>>Many thanks
>>> 
>>>claire
>>> 
>>>
>>>
>>>>plotDeg(eset.f)
>>>
>>>Error in function (classes, fdef, mtable)  : 
>>>        unable to find an inherited method for function "pm", for 
>>>signature "exprSet"
>>>
>>> 
>>>sessionInfo()
>>>R version 2.4.1 (2006-12-18)
>>>i386-pc-mingw32
>>> 
>>>locale:
>>>LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
>>>Kingdom.1252;LC_MONETARY=English_United
>>>Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>>> 
>>>attached base packages:
>>>[1] "splines"   "tools"     "stats"     "graphics"  
>>
>>"grDevices" "utils"
>>
>>>"datasets" 
>>>[8] "methods"   "base"     
>>> 
>>>other attached packages:
>>>hgu133plus2cdf  affycoretools        biomaRt          RCurl
>>>XML 
>>>      "1.14.0"        "1.6.1"        "1.8.2"        "0.8-0"
>>>"1.6-0" 
>>>       GOstats       Category     genefilter       survival
>>>KEGG 
>>>       "2.0.4"        "2.0.3"       "1.12.0"         "2.30"
>>>"1.14.1" 
>>>          RBGL       annotate             GO          graph
>>>limma 
>>>      "1.10.0"       "1.12.1"       "1.14.1"       "1.12.1"
>>>"2.9.13" 
>>>          affy         affyio        Biobase 
>>>      "1.12.2"        "1.2.0"       "1.12.2" 
>>>
>>>
>>>
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>>>Mai...{{dropped}}
>>>
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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.
>>
>>
>> 
>>
> 
> 
> 
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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.