[BioC] affycoretools

[Weiyin Zhou]

Hi Jim,

The help manual is working now after I re-install the package using: 

> source("http://www.bioconductor.org/biocLite.R")
> biocLite("affycoretools")

Thanks for your help,

Weiyin

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Tuesday, December 19, 2006 4:47 PM
To: Weiyin Zhou
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] affycoretools

Weiyin,

That probably means that the help wasn't built correctly. How are you 
installing the package? I just re-installed the package, and I can see 
the help.

Can you see the help when you do help.start()?

Jim

Weiyin Zhou wrote:
> 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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