Dear List members,
I would like to use the affy package to analyze data from MOE430A and
-B
chips. I tried to read in data from both types of chips at once using
data <- ReadAffy(widget=T)
and then reading in 3 MOE430A and 3 MOE430B CEL files.
I got the error message:
"Cel file does not seem to beo of 430MOEA type" when the script tried
to input
data from a 430MOEB Cel file. I had imported the CDF and annotation
packages
for both types of chip.
I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system.
Thanks for any advice/tips!
Peter
You need to deal with each type of chip separately, most of the
normalization/expression estimation procedures work using the values
for the same probes across chips. So it makes no sense to put in two
different types of chips, you need to normalize and compute expression
measure separately - there are some exceptions, in that you could try
to use common probes across both chip types.
Robert
On Mon, Mar 15, 2004 at 01:20:25PM +0100, peter robinson wrote:
> Dear List members,
>
> I would like to use the affy package to analyze data from MOE430A
and -B
> chips. I tried to read in data from both types of chips at once
using
> data <- ReadAffy(widget=T)
> and then reading in 3 MOE430A and 3 MOE430B CEL files.
> I got the error message:
> "Cel file does not seem to beo of 430MOEA type" when the script
tried to input
> data from a 430MOEB Cel file. I had imported the CDF and annotation
packages
> for both types of chip.
> I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system.
>
> Thanks for any advice/tips!
>
> Peter
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
+---------------------------------------------------------------------
------+
| Robert Gentleman phone : (617) 632-5250
|
| Associate Professor fax: (617) 632-2444
|
| Department of Biostatistics office: M1B20
|
| Harvard School of Public Health email: rgentlem@jimmy.harvard.edu
|
+---------------------------------------------------------------------
------+
you need to read in the type A and type B files into separate
affybatch
objects.
eg
my.Data.A <-
ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel"))
my.Data.B <-
ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel"))
Ben
On Mon, 2004-03-15 at 04:20, peter robinson wrote:
> Dear List members,
>
> I would like to use the affy package to analyze data from MOE430A
and -B
> chips. I tried to read in data from both types of chips at once
using
> data <- ReadAffy(widget=T)
> and then reading in 3 MOE430A and 3 MOE430B CEL files.
> I got the error message:
> "Cel file does not seem to beo of 430MOEA type" when the script
tried to input
> data from a 430MOEB Cel file. I had imported the CDF and annotation
packages
> for both types of chip.
> I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system.
>
> Thanks for any advice/tips!
>
> Peter
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
Ben Bolstad <bolstad@stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad
Hi
I am having problems using annaffy GO (aafGO) annotations on these
chips? I
have updated my chip annotation files, and GO library, but still get
> a<-aafGO(rownames(chipA), "moe430a")
Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found
Thanks for your help,
Aedin
-----Original Message-----
From: bioconductor-bounces+aedin.culhane=ucd.ie@stat.math.ethz.ch
[mailto:bioconductor-bounces+aedin.culhane=ucd.ie@stat.math.ethz.ch]On
Behalf Of Ben Bolstad
Sent: 15 March 2004 14:17
To: peter robinson
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] MOE430 A and B
you need to read in the type A and type B files into separate
affybatch
objects.
eg
my.Data.A <-
ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel"))
my.Data.B <-
ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel"))
Ben
On Mon, 2004-03-15 at 04:20, peter robinson wrote:
> Dear List members,
>
> I would like to use the affy package to analyze data from MOE430A
and -B
> chips. I tried to read in data from both types of chips at once
using
> data <- ReadAffy(widget=T)
> and then reading in 3 MOE430A and 3 MOE430B CEL files.
> I got the error message:
> "Cel file does not seem to beo of 430MOEA type" when the script
tried to
input
> data from a 430MOEB Cel file. I had imported the CDF and annotation
packages
> for both types of chip.
> I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system.
>
> Thanks for any advice/tips!
>
> Peter
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
Ben Bolstad <bolstad@stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
I am getting exactly the same error in aafGO:
> a<-aafGO(probeids,"moe430a")
Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found
This is when using version 1.5.0 of the moe430a metadata package. In a
different machine with version 1.4.0 this works alright. annaffy
version
is 1.0.3 in both.
Thanks
Jose
On Mon, 2004-03-15 at 17:04, Aedin wrote:
> Hi
> I am having problems using annaffy GO (aafGO) annotations on these
chips? I
> have updated my chip annotation files, and GO library, but still get
>
> > a<-aafGO(rownames(chipA), "moe430a")
> Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found
>
> Thanks for your help,
> Aedin
>
> -----Original Message-----
> From: bioconductor-bounces+aedin.culhane=ucd.ie@stat.math.ethz.ch
> [mailto:bioconductor-
bounces+aedin.culhane=ucd.ie@stat.math.ethz.ch]On
> Behalf Of Ben Bolstad
> Sent: 15 March 2004 14:17
> To: peter robinson
> Cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] MOE430 A and B
>
>
> you need to read in the type A and type B files into separate
affybatch
> objects.
>
> eg
>
> my.Data.A <-
> ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel"))
>
> my.Data.B <-
> ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel"))
>
> Ben
>
>
>
>
>
>
> On Mon, 2004-03-15 at 04:20, peter robinson wrote:
> > Dear List members,
> >
> > I would like to use the affy package to analyze data from MOE430A
and -B
> > chips. I tried to read in data from both types of chips at once
using
> > data <- ReadAffy(widget=T)
> > and then reading in 3 MOE430A and 3 MOE430B CEL files.
> > I got the error message:
> > "Cel file does not seem to beo of 430MOEA type" when the script
tried to
> input
> > data from a 430MOEB Cel file. I had imported the CDF and
annotation
> packages
> > for both types of chip.
> > I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system.
> >
> > Thanks for any advice/tips!
> >
> > Peter
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> --
> Ben Bolstad <bolstad@stat.berkeley.edu>
> http://www.stat.berkeley.edu/~bolstad
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
Jose Duarte <jose.duarte@anat.ox.ac.uk>
> This is when using version 1.5.0 of the moe430a metadata package. In
a
> different machine with version 1.4.0 this works alright. annaffy
version
> is 1.0.3 in both.
The problem appears to be that there was a difference between the
1.4.x
series of metadata packages and the 1.5.x series which breaks
annaffy-release.
Going back to an earlier message of mine about how we just recently
split
the release/devel metadata packages, this was exactly the sort of
problem
that caused that -> as our metadata packages change on a release cycle
that isn't the same as our software, if we are only offering one
version
of the metadata, it might cause problems with previously released
software.
The problem with the split/rollback a few days ago was that we had
already
been offering the 1.5.0 packages for quite some time and did not want
roll
back further to the 1.4.x series of packages.
One solution, if it is feasible for your needs, is to use the devel
versions of the packages (although in many cases this will require you
to
be using R-1.9.0, currently in alpha stage -> although I believe that
annaffy does not have this restriction). In the meantime, I will look
into the possibility of also providing the 1.4.x data packages.
Thanks
-J
Thanks,
I tried this, but the dev version of annaffy requires utils. So a half
one
version, half the next doesn't work. So I might just download all the
dev
version.
Aedin
-----Original Message-----
From: Jeff Gentry [mailto:jgentry@jimmy.harvard.edu]
Sent: 16 March 2004 17:23
To: Jose Duarte
Cc: Aedin; bioconductor@stat.math.ethz.ch
Subject: RE: [BioC] MOE430 A and B - bug?
> This is when using version 1.5.0 of the moe430a metadata package. In
a
> different machine with version 1.4.0 this works alright. annaffy
version
> is 1.0.3 in both.
The problem appears to be that there was a difference between the
1.4.x
series of metadata packages and the 1.5.x series which breaks
annaffy-release.
Going back to an earlier message of mine about how we just recently
split
the release/devel metadata packages, this was exactly the sort of
problem
that caused that -> as our metadata packages change on a release cycle
that isn't the same as our software, if we are only offering one
version
of the metadata, it might cause problems with previously released
software.
The problem with the split/rollback a few days ago was that we had
already
been offering the 1.5.0 packages for quite some time and did not want
roll
back further to the 1.4.x series of packages.
One solution, if it is feasible for your needs, is to use the devel
versions of the packages (although in many cases this will require you
to
be using R-1.9.0, currently in alpha stage -> although I believe that
annaffy does not have this restriction). In the meantime, I will look
into the possibility of also providing the 1.4.x data packages.
Thanks
-J
It did the trick for me. I installed the dev version of annaffy which
also required the latest annotate. After upgrading both everything
worked fine.
Thanks for all your help
Jose
On Tue, 2004-03-16 at 17:25, Aedin wrote:
> Thanks,
> I tried this, but the dev version of annaffy requires utils. So a
half one
> version, half the next doesn't work. So I might just download all
the dev
> version.
> Aedin
>
> -----Original Message-----
> From: Jeff Gentry [mailto:jgentry@jimmy.harvard.edu]
> Sent: 16 March 2004 17:23
> To: Jose Duarte
> Cc: Aedin; bioconductor@stat.math.ethz.ch
> Subject: RE: [BioC] MOE430 A and B - bug?
>
>
> > This is when using version 1.5.0 of the moe430a metadata package.
In a
> > different machine with version 1.4.0 this works alright. annaffy
version
> > is 1.0.3 in both.
>
> The problem appears to be that there was a difference between the
1.4.x
> series of metadata packages and the 1.5.x series which breaks
> annaffy-release.
>
> Going back to an earlier message of mine about how we just recently
split
> the release/devel metadata packages, this was exactly the sort of
problem
> that caused that -> as our metadata packages change on a release
cycle
> that isn't the same as our software, if we are only offering one
version
> of the metadata, it might cause problems with previously released
> software.
>
> The problem with the split/rollback a few days ago was that we had
already
> been offering the 1.5.0 packages for quite some time and did not
want roll
> back further to the 1.4.x series of packages.
>
> One solution, if it is feasible for your needs, is to use the devel
> versions of the packages (although in many cases this will require
you to
> be using R-1.9.0, currently in alpha stage -> although I believe
that
> annaffy does not have this restriction). In the meantime, I will
look
> into the possibility of also providing the 1.4.x data packages.
>
> Thanks
> -J
Thanks,
I updated the packages annaffy and annotate
(install.packages("annaffy",
CRAN=getOption("BIOC"))), but still get errors
> anncols<-aaf.handler()
> anntableB<-aafTableAnn(pB, "moe430b", anncols)
Error in if (!is.na(go[1])) { : argument is of length zero
In addition: Warning message:
is.na() applied to non-(list or vector) in: is.na(go[1])
> anntableA<-aafTableAnn(pA, "moe430a", anncols)
Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found
Thanks for your help
Aedin
-----Original Message-----
From: Robert Gentleman [mailto:rgentlem@jimmy.harvard.edu]
Sent: 15 March 2004 23:16
To: Aedin
Subject: Re: [BioC] MOE430 A and B
On Mon, Mar 15, 2004 at 05:04:52PM +0000, Aedin wrote:
> Hi
> I am having problems using annaffy GO (aafGO) annotations on these
chips?
I
> have updated my chip annotation files, and GO library, but still get
>
> > a<-aafGO(rownames(chipA), "moe430a")
> Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found
>
Hi there have been some changes to the GO package and these mappings
are no longer needed (and so no longer included). I think if you get
a more recent version of annaffy it may work.
try
install.packages("annaffy")
and then see if that has made things better
Robert
+---------------------------------------------------------------------
------
+
