[Bioc-sig-seq] Package affy and its depencies
Ivan Gregoretti
ivangreg at gmail.com
Wed May 11 21:45:17 CEST 2011
Now it works.
For the record, this is the solution:
######################################################
library(affy)
Data <- ReadAffy(file="/home/johndoe/GSM492799.CEL.gz")
pkg <- cleancdfname(cdfName(Data))
ok <- require(pkg, character.only=TRUE)
if (!ok)
stop(pkg, " not found; install using biocLite?")
eset <- rma(Data)
########################################################
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 3:29 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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<mtmorgan at 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<mtmorgan at fhcrc.org>
>>>> wrote:
>>>>>
>>>>> On 05/11/2011 08:54 AM, Sean Davis wrote:
>>>>>>
>>>>>> On Wed, May 11, 2011 at 11:38 AM, Ivan
>>>>>> Gregoretti<ivangreg at 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
>>>>>>> <jmacdon at 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
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioc-sig-sequencing mailing list
>>>>>>>>> Bioc-sig-sequencing at r-project.org
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>>>>>
>>>>>>>> --
>>>>>>>> James W. MacDonald, M.S.
>>>>>>>> Biostatistician
>>>>>>>> Douglas Lab
>>>>>>>> University of Michigan
>>>>>>>> Department of Human Genetics
>>>>>>>> 5912 Buhl
>>>>>>>> 1241 E. Catherine St.
>>>>>>>> Ann Arbor MI 48109-5618
>>>>>>>> 734-615-7826
>>>>>>>> **********************************************************
>>>>>>>> Electronic Mail is not secure, may not be read every day, and should
>>>>>>>> not
>>>>>>>
>>>>>>> be
>>>>>>>>
>>>>>>>> used for urgent or sensitive issues
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-sig-sequencing mailing list
>>>>>>> Bioc-sig-sequencing at r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>>>>
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-sig-sequencing mailing list
>>>>>> Bioc-sig-sequencing at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>>
>>>>>
>>>>> --
>>>>> Computational Biology
>>>>> Fred Hutchinson Cancer Research Center
>>>>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>>>>
>>>>> Location: M1-B861
>>>>> Telephone: 206 667-2793
>>>>>
>>>
>>>
>>> --
>>> Computational Biology
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>>
>>> Location: M1-B861
>>> Telephone: 206 667-2793
>>>
>
>
> --
> 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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