Hi all,
I was just testing out the affy package with a pair RG-U34A chips. I
get a
series of warnings when using the package, and I can't figure if these
are
something I should be concerned about. I should also note that I
installed R
1.7.0 today and removed my old 1.6.2: not sure if that would make a
difference. The warnings are all identical, so I only show the first
few below.
Is this something to be concerned about, or can I safely ignore it?
Any
comments appreciated,
Paul
> dir();
[1] "U34A_100402_IM01T_LH.CEL" "U34A_100402_IM02T_LH.CEL"
> Data <- ReadAffy();
Warning message:
the condition has length > 1 and only the first element will be used
in: if (dim
(intensity(cel)) != dim.intensity) stop(paste("CEL file dimension
mismatch !\n
(file",
> eset <- rma(Data);
There were 50 or more warnings (use warnings() to see the first 50)
> warnings();
Warning messages:
1: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
2: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
3: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
4: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
5: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
6: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
7: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
8: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
9: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
10: the condition has length > 1 and only the first element will be
used in: if
is.na(ans[[i]])) next
----------------------------------------
This mail sent through www.mywaterloo.ca
Hi again all,
The warnings I detailed below continue with every command I run after
reading
in Cel files via ReadAffy. In addition, I get an error with:
> Data2 <- ReadAffy();
Warning message:
the condition has length > 1 and only the first element will be used
in: if (dim
(intensity(cel)) != dim.intensity) stop(paste("CEL file dimension
mismatch !\n
(file",
> nData2 <- normalize(Data, method="loess");
Error: couldn't find function "predict.loess"
In addition: There were 50 or more warnings (use warnings() to see the
first 50)
> traceback();
6: normalize.loess(intensity(abatch)[Index, ], ...)
5: normalize.AffyBatch.loess(object, ...)
4: do.call(method, alist(object, ...))
3: .local(object, ...)
2: normalize(Data, method = "loess")
1: normalize(Data, method = "loess")
When I ?predict.loess I find it is in the modreg package, which
appears to be
already loaded. Nevertheless, preceding the above commands with
> library(modreg);
Gives the same error message.
Paul
Quoting pcboutro@engmail.uwaterloo.ca:
> Hi all,
>
> I was just testing out the affy package with a pair RG-U34A chips.
I get a
> series of warnings when using the package, and I can't figure if
these are
> something I should be concerned about. I should also note that I
installed R
>
> 1.7.0 today and removed my old 1.6.2: not sure if that would make a
> difference. The warnings are all identical, so I only show the
first few
> below.
>
> Is this something to be concerned about, or can I safely ignore it?
Any
> comments appreciated,
> Paul
>
>
> > dir();
> [1] "U34A_100402_IM01T_LH.CEL" "U34A_100402_IM02T_LH.CEL"
>
> > Data <- ReadAffy();
> Warning message:
> the condition has length > 1 and only the first element will be used
in: if
> (dim
> (intensity(cel)) != dim.intensity) stop(paste("CEL file dimension
mismatch
> !\n
> (file",
>
> > eset <- rma(Data);
> There were 50 or more warnings (use warnings() to see the first 50)
> > warnings();
> Warning messages:
> 1: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 2: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 3: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 4: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 5: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 6: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 7: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 8: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 9: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
> 10: the condition has length > 1 and only the first element will be
used in:
> if
> is.na(ans[[i]])) next
>
>
> ----------------------------------------
> This mail sent through www.mywaterloo.ca
>
----------------------------------------
This mail sent through www.mywaterloo.ca
These warnings have been eliminated in the current development affy
packages. You will likely get a lot of these type of warnings when you
use the 1.1 release affy package with R 1.7.0
Thanks,
Ben
> Hi again all,
>
> The warnings I detailed below continue with every command I run
after reading
> in Cel files via ReadAffy. In addition, I get an error with:
>
> > Data2 <- ReadAffy();
> Warning message:
> the condition has length > 1 and only the first element will be used
in: if (dim
> (intensity(cel)) != dim.intensity) stop(paste("CEL file dimension
mismatch !\n
> (file",
>
> > nData2 <- normalize(Data, method="loess");
> Error: couldn't find function "predict.loess"
> In addition: There were 50 or more warnings (use warnings() to see
the first 50)
>
> > traceback();
> 6: normalize.loess(intensity(abatch)[Index, ], ...)
> 5: normalize.AffyBatch.loess(object, ...)
> 4: do.call(method, alist(object, ...))
> 3: .local(object, ...)
> 2: normalize(Data, method = "loess")
> 1: normalize(Data, method = "loess")
>
> When I ?predict.loess I find it is in the modreg package, which
appears to be
> already loaded. Nevertheless, preceding the above commands with
> > library(modreg);
>
> Gives the same error message.
> Paul
>
> Quoting pcboutro@engmail.uwaterloo.ca:
>
> > Hi all,
> >
> > I was just testing out the affy package with a pair RG-U34A chips.
I get a
> > series of warnings when using the package, and I can't figure if
these are
> > something I should be concerned about. I should also note that I
installed R
> >
> > 1.7.0 today and removed my old 1.6.2: not sure if that would make
a
> > difference. The warnings are all identical, so I only show the
first few
> > below.
> >
> > Is this something to be concerned about, or can I safely ignore
it? Any
> > comments appreciated,
> > Paul
> >
> >
> > > dir();
> > [1] "U34A_100402_IM01T_LH.CEL" "U34A_100402_IM02T_LH.CEL"
> >
> > > Data <- ReadAffy();
> > Warning message:
> > the condition has length > 1 and only the first element will be
used in: if
> > (dim
> > (intensity(cel)) != dim.intensity) stop(paste("CEL file dimension
mismatch
> > !\n
> > (file",
> >
> > > eset <- rma(Data);
> > There were 50 or more warnings (use warnings() to see the first
50)
> > > warnings();
> > Warning messages:
> > 1: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 2: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 3: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 4: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 5: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 6: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 7: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 8: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 9: the condition has length > 1 and only the first element will be
used in:
> > if
> > is.na(ans[[i]])) next
> > 10: the condition has length > 1 and only the first element will
be used in:
> > if
> > is.na(ans[[i]])) next
> >
> >
> > ----------------------------------------
> > This mail sent through www.mywaterloo.ca
> >
>
>
>
>
> ----------------------------------------
> This mail sent through www.mywaterloo.ca
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
Ben Bolstad <bolstad@stat.berkeley.edu>
Okay, that makes sense. Just two more questions, then:
1. Do you have a guess-timate date for the next release?
2. Can I mix-and-match production/development modules, or will I need
to
download pretty much the whole development release to take advantage
of changes
in the affy package?
Thanks for the help,
Paul
Quoting Ben Bolstad <bolstad@stat.berkeley.edu>:
> These warnings have been eliminated in the current development affy
> packages. You will likely get a lot of these type of warnings when
you
> use the 1.1 release affy package with R 1.7.0
>
> Thanks,
>
> Ben
>
>
>
>
>
>
> > Hi again all,
> >
> > The warnings I detailed below continue with every command I run
after
> reading
> > in Cel files via ReadAffy. In addition, I get an error with:
> >
> > > Data2 <- ReadAffy();
> > Warning message:
> > the condition has length > 1 and only the first element will be
used in: if
> (dim
> > (intensity(cel)) != dim.intensity) stop(paste("CEL file dimension
mismatch
> !\n
> > (file",
> >
> > > nData2 <- normalize(Data, method="loess");
> > Error: couldn't find function "predict.loess"
> > In addition: There were 50 or more warnings (use warnings() to see
the
> first 50)
> >
> > > traceback();
> > 6: normalize.loess(intensity(abatch)[Index, ], ...)
> > 5: normalize.AffyBatch.loess(object, ...)
> > 4: do.call(method, alist(object, ...))
> > 3: .local(object, ...)
> > 2: normalize(Data, method = "loess")
> > 1: normalize(Data, method = "loess")
> >
> > When I ?predict.loess I find it is in the modreg package, which
appears to
> be
> > already loaded. Nevertheless, preceding the above commands with
> > > library(modreg);
> >
> > Gives the same error message.
> > Paul
> >
> > Quoting pcboutro@engmail.uwaterloo.ca:
> >
> > > Hi all,
> > >
> > > I was just testing out the affy package with a pair RG-U34A
chips. I get
> a
> > > series of warnings when using the package, and I can't figure if
these
> are
> > > something I should be concerned about. I should also note that
I
> installed R
> > >
> > > 1.7.0 today and removed my old 1.6.2: not sure if that would
make a
> > > difference. The warnings are all identical, so I only show the
first
> few
> > > below.
> > >
> > > Is this something to be concerned about, or can I safely ignore
it? Any
>
> > > comments appreciated,
> > > Paul
> > >
> > >
> > > > dir();
> > > [1] "U34A_100402_IM01T_LH.CEL" "U34A_100402_IM02T_LH.CEL"
> > >
> > > > Data <- ReadAffy();
> > > Warning message:
> > > the condition has length > 1 and only the first element will be
used in:
> if
> > > (dim
> > > (intensity(cel)) != dim.intensity) stop(paste("CEL file
dimension
> mismatch
> > > !\n
> > > (file",
> > >
> > > > eset <- rma(Data);
> > > There were 50 or more warnings (use warnings() to see the first
50)
> > > > warnings();
> > > Warning messages:
> > > 1: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 2: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 3: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 4: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 5: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 6: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 7: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 8: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 9: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > > 10: the condition has length > 1 and only the first element will
be used
> in:
> > > if
> > > is.na(ans[[i]])) next
> > >
> > >
> > > ----------------------------------------
> > > This mail sent through www.mywaterloo.ca
> > >
> >
> >
> >
> >
> > ----------------------------------------
> > This mail sent through www.mywaterloo.ca
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> --
> Ben Bolstad <bolstad@stat.berkeley.edu>
>
----------------------------------------
This mail sent through www.mywaterloo.ca
> 1. Do you have a guess-timate date for the next release?
Roughly a month would be my guess. Plus or minus a year or two ;)
> 2. Can I mix-and-match production/development modules, or will I
need to
> download pretty much the whole development release to take advantage
of changes
> in the affy package?
Packages that are required by affy you should have the appropriate
versions for. Eyeballing it, this would mean to me that BIobase &
tkWidgets need to be devel versions - but that might not be 100%
true. Look at the "Depends" field in the DESCRIPTION file (or, look
at
the 'affy' link in both the 'release 1.1 packages' and 'developmental
packages' link on our website).
-Jeff
Hi.
Has anyone used the GenePlotter package on the mgu74Av2 affymetrix
array?
I have been unable to figure out how to extract the chromosomal
location for the probesets from the data package for the u74 chip. Is
this
information built into that data package? If not, could someone please
point me to how one might go about compiling the required data?
Thanks!
Jeff.
__________________________________
Jeffrey Rasmussen
Research Consultant, Bioinformatics
Department of Immunology
University of Washington
