There are several issues here.  First, you are describing problems
installing Bioconductor software that relate to your internet connectivity
and have nothing to do with Bioconductor.

Error in download.file(url, destfile, method, mode = "wb", ...) :
 cannot open URL '

that indicates a general problem that may be avoided by starting R with an
--internet2 switch, but you should talk to a systems support person there to
get advice relevant to your setup.

Second, you are asking about exon array analysis, and there are several
approaches available.  The "documentation" tab of the Bioconductor web site
shows a "workflows" node, and this takes you to

http://www.bioconductor.org/docs/workflows/oligoarrays/

where the main options are described.  That page may need a little updating
as exonmap has been replaced by xmapcore (yes, the xmapcore primer refers to
exonmap as deprecated).  The xps system will require installation of CERN
ROOT infrastructure.  The oligo approach may have the lightest external
infrastructure requirements and a focused analysis illustration is given in
the overview vignette

http://www.bioconductor.org/packages/2.6/bioc/vignettes/oligo/inst/doc/V1Overview.pdf

Section 3 in particular takes you through the import and preprocessing of
some exon arrays (that you must download yourself from affymetrix), all the
way to visualizing expression patterns over a gene model for a specific
gene; the workflow involves biomaRt, annotationDbi, Biostrings, and
GenomeGraphs.

I would suggest that exon array analysis is not an activity with which one
should START using bioconductor.  IMHO, mastery of general issues with array
import and quality assessment, general tasks of annotation and identifier
resolution, and statistics of differential expression at the gene level
should be acquired before getting involved with exon arrays.



On Wed, May 26, 2010 at 3:00 AM, l.mohammadikhankahdani <
l.mohammadikhankahdani@erasmusmc.nl> wrote:

>
> Does anyone have experience with exon array analysis?
> If so, do you know how to install huex10stv2cdf package?
>
> best
> Leila
>
>
>
> on 2010/05/26 10:38 AM mahalakshmi sivamani said the following:
>
>> Hi,
>>
>> While trying to install hgu133acdf- windows package in R i am getting the
>> following error and unable to install the same.
>>
>>  source("http://bioconductor.org/biocLite.R")
>>>    biocLite("hgu133acdf")
>>>
>> Using R version 2.10.0, biocinstall version 2.5.10.
>> Installing Bioconductor version 2.5 packages:
>> [1] "hgu133acdf"
>> Please wait...
>>
>> trying URL '
>>
>> http://www.bioconductor.org/packages/2.5/data/annotation/bin/windows/contrib/2.10/hgu133acdf_2.5.0.zip
>> '
>> Error in download.file(url, destfile, method, mode = "wb", ...) :
>>  cannot open URL '
>>
>> http://www.bioconductor.org/packages/2.5/data/annotation/bin/windows/contrib/2.10/hgu133acdf_2.5.0.zip
>> '
>> In addition: Warning message:
>> In download.file(url, destfile, method, mode = "wb", ...) :
>>  cannot open: HTTP status was '0 (nil)'
>> Warning in download.packages(pkgs, destdir = tmpd, available = available,
>>  :
>>  download of package 'hgu133acdf' failed
>>
>> Is there any possibilities of getting out from this problem.
>>
>> Please do the needful. Thanks in advance.
>>
>> Regards,
>>
>> S.Mahalakshmi
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
> _______________________________________________
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>

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