Hi, Fellows:
I want to install bioconductor on Sun, machine hardware sun4u, version
5.9
operator system, sparc processor. After I loaded affy, I met some
issues:
>library(affy)
Loading required package: tkWidgets
Loading required package: widgetTools
Loading required package: tcltk
Error in firstlib(which.lib.loc, package) :
Tcl/Tk support is not available on this system
Error: package 'tcltk' could not be loaded
>list.celfiles()
Error: couldn't find function "list.celfiles"
It seems all commends from affy can not work here. Why? any help from
you
would be greatly appriated. Thanks.
John
Hi John,
The output you sent indicates that the tcltk package is required for
use
of affy. For the tcltk R package to work, you have to install Tcl/Tk
libraries on the system.
Try installing Tcl/Tk and then trying again.
+ seth
On Wed, Jan 12, 2005 at 02:19:01PM -0700, Jiuzhou song wrote:
> Hi, Fellows:
> I want to install bioconductor on Sun, machine hardware sun4u,
version 5.9
> operator system, sparc processor. After I loaded affy, I met some
issues:
> >library(affy)
> Loading required package: tkWidgets
> Loading required package: widgetTools
> Loading required package: tcltk
> Error in firstlib(which.lib.loc, package) :
> Tcl/Tk support is not available on this system
> Error: package 'tcltk' could not be loaded
> >list.celfiles()
> Error: couldn't find function "list.celfiles"
I would like to ask whether there is a cdf file available for the
Arabidopsis 8K Affymetrix chip (the first one). I would like to
normalize data with RMA software.
Thank you in advance
MInes
Mines,
I'm not familiar with the arabidopsis chips, but you did check
(http://www.bioconductor.org/data/metaData.html) and didn't find it?
Sean
On Jan 17, 2005, at 12:33 PM, Maria Ines Zanor wrote:
> I would like to ask whether there is a cdf file available for the
> Arabidopsis 8K Affymetrix chip (the first one). I would like to
> normalize data with RMA software.
> Thank you in advance
>
> MInes
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
Sean Davis wrote:
> Mines,
>
> I'm not familiar with the arabidopsis chips, but you did check
> (http://www.bioconductor.org/data/metaData.html) and didn't find it?
She shouldn't even need to check. The affy package has automagic
download of necessary cdfenvs, so all that is needed is something
like:
abatch <- ReadAffy()
abatch
If the cdfenv isn't available, it will error out. Otherwise the
correct
one will be downloaded and installed for you.
Jim
>
> Sean
>
> On Jan 17, 2005, at 12:33 PM, Maria Ines Zanor wrote:
>
>> I would like to ask whether there is a cdf file available for the
>> Arabidopsis 8K Affymetrix chip (the first one). I would like to
>> normalize data with RMA software.
>> Thank you in advance
>>
>> MInes
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
