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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University of Michigan
Department of Human Genetics
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Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

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