[BioC] affycoretools

[Weiyin Zhou]

Jim,

?scan link works.  But not for the help links from affycoretools.

Here is my session info.
> sessionInfo()
R version 2.4.0 (2006-10-03) 
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] "tcltk"     "splines"   "tools"     "methods"   "stats"
"graphics" 
 [7] "grDevices" "utils"     "datasets"  "base"     

other attached packages:
        pcaMethods                pls            ellipse
MASS 
           "1.2.2"            "1.2-1"            "0.3-4"
"7.2-30" 
ehtapops520389fcdf          affylmGUI      affycoretools
biomaRt 
          "1.12.0"            "1.5.4"            "1.6.0"
"1.8.1" 
             RCurl                XML            GOstats
Category 
           "0.8-0"            "1.3-2"            "2.0.4"
"2.0.3" 
        genefilter           survival               KEGG
RBGL 
          "1.12.0"             "2.30"           "1.12.0"
"1.10.0" 
          annotate                 GO              graph
limma 
          "1.12.0"           "1.14.1"           "1.12.0"
"2.9.1" 
              affy             affyio            Biobase 
          "1.12.1"            "1.2.0"           "1.12.2" 

Weiyin

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Tuesday, December 19, 2006 4:35 PM
To: Weiyin Zhou
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] affycoretools

Hi Weiyin,

Weiyin Zhou wrote:
> Jim,
> 
> Thank,
> 
> ?plotPCA does not work for me. 

I'm not sure what 'does not work' means. You are going to have to give a

better hint than that if you want some help. Probably giving the output 
of sessionInfo() would be useful as well.

Does any help work? How about ?scan

Jim


> 
> Weiyin
> 
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: Tuesday, December 19, 2006 2:59 PM
> To: Weiyin Zhou
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] affycoretools
> 
> Weiyin Zhou wrote:
> 
>>Hi Jim,
>>
>>I am trying to consult the help page for the affycoretools package to
> 
> do
> 
>>a screeplot.  However, all the links are nor working.  Could you or
>>someone tell me the format for this plot function?
> 
> 
> Does ?plotPCA not work for you?
> 
> Anyway, the argument would be plotPCA(eset, screeplot=TRUE)
> 
> Best,
> 
> Jim
> 
> 
> 
>>Thanks in advance,
>>
>>Weiyin
> 
> 
> 


-- 
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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