On 05/11/2011 12:19 PM, Ivan Gregoretti wrote:
Well, if I do annPkgName(annotation(Data)), I get
"mouse4302.db"
My mistake; I think you want cleancdfname(cdfName(Data)). Martin
Now, even though I do library(mouse4302.db), I still get the same
cdfname warning.
This behaviour seems not to be new:
https://stat.ethz.ch/pipermail/bioconductor/2009-January/025787.html
In case anybody is interested, here is the link to the CEL file:
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM492nnn/GSM492799/GSM492799%2ECEL%2Egz
So, I am not quite there yet.
Thank you,
Ivan
Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878
On Wed, May 11, 2011 at 2:59 PM, Martin Morgan<mtmor...@fhcrc.org> wrote:
On 05/11/2011 11:51 AM, Ivan Gregoretti wrote:
Hello Martin,
When I do annotation(Data) I get the response
"mouse4302"
What would you do now?
maybe
library(annotate)
pkg<- annPkgName(annotation(Data))
ok<- require(pkg, character.only=TRUE)
if (!ok)
stop(pkg, " not found; install using biocLite?")
Thank you,
Ivan
Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878
On Wed, May 11, 2011 at 1:29 PM, Martin Morgan<mtmor...@fhcrc.org> wrote:
On 05/11/2011 08:54 AM, Sean Davis wrote:
On Wed, May 11, 2011 at 11:38 AM, Ivan
Gregoretti<ivang...@gmail.com>wrote:
Hello Jim,
First, thank you for responding.
Indeed, the issue is the request to generate a personal library.
I use a wide variety of Bioconductor packages, from the most canonical
ones like ShortRead to more obscure ones like cosmo, however, no
function ever asked me to create a personal library as a condition for
execution.
Do you regularly encounter functions that make such demand? I am
curious.
Hi, Ivan.
This request is from R, itself, and not from the affy package or any
other
Actually, rma needs the cdf package corresponding to the chip, and calls
getCdfInfo and eventually cdfFromBioC if it is not installed. This is
apparently determined by getOption("BioC")$affy$probesloc, but this is
not
well-documented (which is an understatment). A work-around would make
sure
the package (from annotation(Data)) is installed before calling rma(),
and
then you'd at least have more control over what to do if prompted.
just.rma is a (much) more memory efficient approach if the goal is to
arrive
directly at an ExpressionSet without needing the AffyBatch.
Martin
package. If you haven't seen this before, it was probably because a
user
Library existed previously (you are asked only the first time it is
needed)
or because the default system package location was writeable by you.
See
the R manuals for details on library locations if you want more detail.
Sean
Thank you,
Ivan
PS: By the way, cosmo rocks.
Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878
On Tue, May 10, 2011 at 7:30 PM, James W. MacDonald
<jmac...@med.umich.edu> wrote:
Hi Ivan,
On 5/10/2011 4:41 PM, Ivan Gregoretti wrote:
There seems to be a dependency error that comes up when running an
analysis with affy. It only takes three commands.
###################################################################
library(affy)
Data<- ReadAffy(file="/home/johndoe/GSM492799.CEL.gz")
eset<- rma(Data)
Warning in install.packages(cdfname, lib = lib, repos =
Biobase:::biocReposList(), :
'lib = "/usr/local/lib64/R/library"' is not writable
Would you like to create a personal library
~/R/x86_64-unknown-linux-gnu-library/2.14
to install packages into? (y/n)
###################################################################
Is this error reproducible by others?
I don't see an error here. But perhaps you are referring to the
warning?
I'm not sure how it could be made clearer, however. The gist is that
you
are
running R as non-root (as you should), and therefore don't have write
access
to the /usr/local/lib64/R/library, (which you should not), so R is
stating
that fact and asking you if you want it to create a personal library
in
your
home directory, where in future it will look for any packages that
aren't
found in the 'usual' place.
So, long story short, if you had simply typed a 'y' after that
warning,
you
would have got the package downloaded and gone about your business.
Best,
Jim
Thank you
Ivan
sessionInfo()
R version 2.14.0 Under development (unstable) (2011-04-14 r55450)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] affy_1.31.1 Biobase_2.13.1
loaded via a namespace (and not attached):
[1] affyio_1.21.0 preprocessCore_1.15.0 tools_2.14.0
Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878
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Computational Biology
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Location: M1-B861
Telephone: 206 667-2793
--
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