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@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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
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.
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Jim,
Thank,
?plotPCA does not work for me.
Weiyin
-----Original Message-----
From: James W. MacDonald [mailto:jmacdon@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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not
be used for urgent or sensitive issues.
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
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@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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not
be used for urgent or sensitive issues.
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
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@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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not
be used for urgent or sensitive issues.
