[BioC] affycoretools

[Weiyin Zhou]

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?

Thanks in advance,

Weiyin

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Friday, December 15, 2006 1:10 PM
To: Weiyin Zhou
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] affycoretools

Hi Weiyin,

I wonder if there is a problem with your annaffy package. Try 
re-installing it and see if that fixes the problem.

Best,

Jim

Weiyin Zhou wrote:
> Hi,
> 
>  
> 
> When I try to load package "affycoretools", I get follow error
messages:
> 
>  
> 
> 
>>local({pkg <- select.list(sort(.packages(all.available = TRUE)))
> 
> 
> + if(nchar(pkg)) library(pkg, character.only=TRUE)})
> 
> Loading required package: limma
> 
> Loading required package: GOstats
> 
> Loading required package: graph
> 
> Loading required package: GO
> 
> Loading required package: annotate
> 
> Loading required package: RBGL
> 
> Loading required package: Category
> 
> Loading required package: KEGG
> 
> Loading required package: genefilter
> 
> Loading required package: survival
> 
> Loading required package: splines
> 
> Loading required package: biomaRt
> 
> Loading required package: XML
> 
>  
> 
> Attaching package: 'XML'
> 
>  
> 
>  
> 
>         The following object(s) are masked from package:graph :
> 
>  
> 
>          addNode 
> 
>  
> 
> Loading required package: RCurl
> 
>  
> 
> Attaching package: 'biomaRt'
> 
>  
> 
>  
> 
>         The following object(s) are masked from package:annotate :
> 
>  
> 
>          getGO 
> 
>  
> 
> Error in loadNamespace(i, c(lib.loc, .libPaths())) : 
> 
>         in 'annaffy' methods specified for export, but none defined:
[,
> [[, colnames, colnames<-, getCSS, getHTML, getTD, getText, getURL,
> probeids, probeids<-, saveHTML, saveText, show
> 
> Error: package/namespace load failed for 'affycoretools'
> 
>  
> 
>  
> 
> 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] "splines"   "tools"     "methods"   "stats"     "graphics"
> "grDevices"
> 
> [7] "utils"     "datasets"  "base"     
> 
>  
> 
> other attached packages:
> 
>    biomaRt      RCurl        XML    GOstats   Category genefilter
> survival 
> 
>    "1.8.1"    "0.8-0"    "1.3-2"    "2.0.4"    "2.0.3"   "1.12.0"
> "2.30" 
> 
>       KEGG       RBGL   annotate         GO      graph      limma
> affy 
> 
>   "1.12.0"   "1.10.0"   "1.12.0"   "1.14.1"   "1.12.0"    "2.9.1"
> "1.12.1" 
> 
>     affyio    Biobase 
> 
>    "1.2.0"   "1.12.2"
> 
>  
> 
> Thanks in advance, 
> 
> Weiyin Zhou
> 
> Statistics and Data Analyst
> 
> ExonHit Therapeutics, Inc.
> 
> 217 Perry Parkway, Building # 5
> 
> Gaithersburg, MD 20877
> 
>  
> 
> email: Weiyin.zhou at exonhit-usa.com
<mailto:Weiyin.zhou at exonhit-usa.com> 
> 
> phone: 240.404.0184
> 
> fax: 240.683.7060
> 
>  
> 
>  
> 
>  
> 
> 
> 	[[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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