Hello,
I am trying to read some .CEL files using the
ReadAffy() function of the Affy library. I am getting
the following error:
Data1<-ReadAffy()
Error in "intensity<-"(*tmp*, value =
c(intensity(cel))) :
couldn't find function "exprs<-"
Please can somebody help me understand this error. Is
there a way (some documentation
available )by which I can undertand these errors
myself.
Thanking you,
Tapan Mehta
Hi Tapan,
which versions of the packages "Biobase" and "affy" are you using?
To understand the error message you're getting, have a look at the
function "showMethods", and the definitions of the exprSet and
AffyBatch
classes in the R subdirectories of the above-mentioned packages.
Best -
Wolfgang
-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax: +49 6221 42524709
Http: www.dkfz.de/mga/whuber
-------------------------------------
On Tue, 20 May 2003, Tapan Mehta wrote:
> Hello,
>
> I am trying to read some .CEL files using the
> ReadAffy() function of the Affy library. I am getting
> the following error:
>
> Data1<-ReadAffy()
> Error in "intensity<-"(*tmp*, value =
> c(intensity(cel))) :
> couldn't find function "exprs<-"
>
> Please can somebody help me understand this error. Is
> there a way (some documentation
> available )by which I can undertand these errors
> myself.
>
> Thanking you,
>
> Tapan Mehta
>
Hello,
Thank you for your quick reply. I am using R1.6.1 and
the I am getting a warning saying the following:
package affy was built under R version 1.7.0
Do you think it is just a version problem ?It would be
nice if you could elaborate how the showMethods will
help me in tackling this problem.
Tapan Mehta
--- w.huber@dkfz-heidelberg.de wrote:
>
> Hi Tapan,
>
> which versions of the packages "Biobase" and "affy"
> are you using?
>
> To understand the error message you're getting, have
> a look at the
> function "showMethods", and the definitions of the
> exprSet and AffyBatch
> classes in the R subdirectories of the
> above-mentioned packages.
>
> Best -
> Wolfgang
>
> -------------------------------------
> Wolfgang Huber
> Division of Molecular Genome Analysis
> German Cancer Research Center
> Heidelberg, Germany
> Phone: +49 6221 424709
> Fax: +49 6221 42524709
> Http: www.dkfz.de/mga/whuber
> -------------------------------------
>
>
> On Tue, 20 May 2003, Tapan Mehta wrote:
>
> > Hello,
> >
> > I am trying to read some .CEL files using the
> > ReadAffy() function of the Affy library. I am
> getting
> > the following error:
> >
> > Data1<-ReadAffy()
> > Error in "intensity<-"(*tmp*, value =
> > c(intensity(cel))) :
> > couldn't find function "exprs<-"
> >
> > Please can somebody help me understand this error.
> Is
> > there a way (some documentation
> > available )by which I can undertand these errors
> > myself.
> >
> > Thanking you,
> >
> > Tapan Mehta
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
>
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
Hi Tapan,
> Do you think it is just a version problem?
It could be a version problem of the packages Biobase and affy.
Unfortunately you have not answered my question in your mail. Perhaps
you
are using an "old" Biobase and a more recent ("development") affy?
> It would be nice if you could elaborate how the showMethods will
help me
> in tackling this problem.
Before going down this path, please download the most recent developer
versions of BOTH affy and Biobase (which are pretty stable and will
turn
into "release" versions in a very short time from now), and try again.
Use
getBioC("all", relLevel="devel")
with the script getBioC.R from the webpage.
Best regards
Wolfgang
-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax: +49 6221 42524709
Http: www.dkfz.de/mga/whuber
-------------------------------------
On Tue, 20 May 2003, Tapan Mehta wrote:
> Hello,
>
> Thank you for your quick reply. I am using R1.6.1 and
> the I am getting a warning saying the following:
>
> package affy was built under R version 1.7.0
>
>
> Thank you for your quick reply. I am using R1.6.1 and
> the I am getting a warning saying the following:
> package affy was built under R version 1.7.0
If you're using the affy from the development branch (which I believe
you
are as the affy packages from Release 1.1 are reporting themselves as
being built under 1.6.2), then you really should be using R-1.7.0 (to
be
more specific, you *really* should be using the patched version of
R-1.7.0), as that is their target platform.
-J
Hello,
Thank you for your help. I have now installed the
latest developmental versions. This also does not seem
to have solved the problem. I tried to install the
development version but the problem still exists.
Before I start the ReadAffy() funcion I get a warning
saying
package affy was built under R version 1.6.2
2: package Biobase was built under R version 1.6.2
Do you think I need to go for complete change in the
versions?
After the developmental versions failed to remove the
error I tried to install the previous release of the
affy and the biobase corresopnding to R1.6.1. While
the biobase got installed properly , affy did not and
gave me the following error.
install.packages("C:/Documents and
Settings/TMehta/Desktop/Installers/affy_1.0.2.zip",
.libPaths()[1], CRAN = NULL)
Error in zip.unpack(pkg, lib) : cannot open file
C:/PROGRA~1/R/rw1061/library/affy/libs/affy.dll
PLease guide me.
Thanking you,
Tapan Mehta
--- Jeff Gentry <jgentry@jimmy.harvard.edu> wrote:
> > Thank you for your quick reply. I am using R1.6.1
> and
> > the I am getting a warning saying the following:
> > package affy was built under R version 1.7.0
>
> If you're using the affy from the development branch
> (which I believe you
> are as the affy packages from Release 1.1 are
> reporting themselves as
> being built under 1.6.2), then you really should be
> using R-1.7.0 (to be
> more specific, you *really* should be using the
> patched version of
> R-1.7.0), as that is their target platform.
>
> -J
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
>
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
