Hi,
I am trying to use affy package.
library(affy)
Data<-ReadAffy()
eset<-rma(Data)
Then I found the following message:
Error in .;ocal(object, which, ...) : couldn't find function
"multiget"
And I tried to search "multiget" functions with no success. I must
missed some
packages from bioconductor. Could you tell me which package "multiget"
belongs.
BTW, I can't install bioconductor through getBioC() due to some
firewall
settings. So what I did is dowload each packages on my local machine,
then
install packages individually locally. Do i missed anythings here? And
I also
installed every packages "Affy" depended such as Biobase, reposTools,
tkWidgets.
Thanks.
Nan
> I am trying to use affy package.
>From 'devel' or 'release1.4'?
> And I tried to search "multiget" functions with no success. I must
missed some
> packages from bioconductor. Could you tell me which package
"multiget"
> belongs.
The multiget function exists in Biobase for release1.4, but will throw
a
warning on usage (as it was deprecated). It does not exist at all in
BioC-devel (in favor of using R's 'mget()' function).
> install packages individually locally. Do i missed anythings here?
And I also
> installed every packages "Affy" depended such as Biobase,
reposTools,
> tkWidgets.
Again - which version of affy, Biobase, etc ... from devel or
release1.4?
If you encountered this problem in the release1.4 version, you
definitely
should let the maintainers of the affy package know about this.
Actually,
even if you encountered it in the devel version, you should let them
know.
-J
The bioconductor is from release 1.4. And the affy is version 1.5.0.
Biobase_1.4.16. I definitely installed and loaded Biobase. Is this
only me
that get this error message? The maintainers is on this email list,
right?
Nan
>===== Original Message From Jeff Gentry <jgentry@jimmy.harvard.edu>
=====
>> I am trying to use affy package.
>
>From 'devel' or 'release1.4'?
>
>> And I tried to search "multiget" functions with no success. I must
missed
some
>> packages from bioconductor. Could you tell me which package
"multiget"
>> belongs.
>
>The multiget function exists in Biobase for release1.4, but will
throw a
>warning on usage (as it was deprecated). It does not exist at all in
>BioC-devel (in favor of using R's 'mget()' function).
>
>> install packages individually locally. Do i missed anythings here?
And I
also
>> installed every packages "Affy" depended such as Biobase,
reposTools,
>> tkWidgets.
>
>Again - which version of affy, Biobase, etc ... from devel or
release1.4?
>
>If you encountered this problem in the release1.4 version, you
definitely
>should let the maintainers of the affy package know about this.
Actually,
>even if you encountered it in the devel version, you should let them
know.
>
>-J
> The bioconductor is from release 1.4. And the affy is version 1.5.0.
> Biobase_1.4.16. I definitely installed and loaded Biobase. Is this
only me
The release 1.4 version of affy is '1.4.32' and the release 1.4
version of
Biobase is '1.4.15'. The current devel version of affy is '1.5.2' and
Biobase is '1.4.16'.
So, you're definitely using the devel version of the software. I
suspect
that if you updated to the latest devel affy, that this problem would
go
away (I believe that they had a multiget in a slightly older version),
or
if you do indeed want to use the 1.4 release versions, switch to using
those and that should also solve the problem.
Jeff, You are cool. Thanks very much. After using all the packages
from
release 4, there is no problem.
Nan
>===== Original Message From Jeff Gentry <jgentry@jimmy.harvard.edu>
=====
>> The bioconductor is from release 1.4. And the affy is version
1.5.0.
>> Biobase_1.4.16. I definitely installed and loaded Biobase. Is this
only me
>
>The release 1.4 version of affy is '1.4.32' and the release 1.4
version of
>Biobase is '1.4.15'. The current devel version of affy is '1.5.2'
and
>Biobase is '1.4.16'.
>
>So, you're definitely using the devel version of the software. I
suspect
>that if you updated to the latest devel affy, that this problem would
go
>away (I believe that they had a multiget in a slightly older
version), or
>if you do indeed want to use the 1.4 release versions, switch to
using
>those and that should also solve the problem.