[BioC] ai<-compute.affinities(mm430mmentrezg7)

[James W. MacDonald]

The only way to choose the version is to go to the MBNI website and 
download the one you want. BioC only carries the most current version.

Best,

Jim



Radek Blatny wrote:
> Oh, I've figured it out, the command must be:
> 
> AffyBatch at cdfName<-"mm430mmentrezg"
> 
> not
> 
> AffyBatch at cdfName<-"mm430mmentrezg7"
> 
> I thought I can choose the genome version by appending the number. 
> Anyway, is there a way to choose the version?
> 
> Regards, Radek
> 
> On Aug 12, 2008, at 6:07 PM, Radek Blatny wrote:
> 
> R> sessionInfo()
> R version 2.6.0 Patched (2007-10-22 r43252)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C 
> 
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
>  [1] mouse4302_2.0.1            mm430mmentrezgprobe_10.0.0
>  [3] mm430mmentrezg_10.0.0      mouse4302probe_2.0.0
>  [5] mouse4302cdf_2.0.0         geneplotter_1.16.0
>  [7] lattice_0.17-12            annotate_1.16.1
>  [9] xtable_1.5-2               AnnotationDbi_1.0.6
> [11] RSQLite_0.6-9              DBI_0.2-4
> [13] vsn_3.2.1                  limma_2.12.0
> [15] affyPLM_1.14.0             RColorBrewer_1.0-2
> [17] simpleaffy_2.14.05         gcrma_2.10.0
> [19] matchprobes_1.10.0         genefilter_1.16.0
> [21] survival_2.34-1            affy_1.16.0
> [23] preprocessCore_1.0.0       affyio_1.6.1
> [25] Biobase_1.16.3
> 
> loaded via a namespace (and not attached):
> [1] grid_2.6.0         KernSmooth_2.22-22 rcompgen_0.1-17
> 
> ####################################################
> 
> # I am trying to change the cdf file from Mouse430_2 to mm430mmentrezg7:
> 
> AffyBatch at cdfName<-"mm430mmentrezg7"
> 
> # and afterwards to initiate the affinity computation and continue with 
> gcrma, but I am getting the error:
> 
> R> ai<-compute.affinities(cdfName(Data))
> 
> Computing affinitiesError in getCDF(cdfpackagename) :
>   The current operation could not access the Bioconductor repository. 
> Please check your internet connection, and report further problems to 
> bioconductor at stat.math.ethz.ch
> In addition: Warning message:
> In readLines(biocURL) : cannot open: HTTP status was '404 Not Found'
> 
> 
> 
> 
> Regards, Radek
> 
> 
> 
> On Aug 12, 2008, at 5:43 PM, Sean Davis wrote:
> 
> On Tue, Aug 12, 2008 at 10:58 AM, Radek Blatny <blatny at img.cas.cz> wrote:
>> Hi, I'm getting the error, although my connection is OK.
>>
>> R> ai<-compute.affinities(cdfName(Data))
>> Computing affinitiesError in getCDF(cdfpackagename) :
>>  The current operation could not access the Bioconductor repository. 
>> Please
>> check your internet connection, and report further problems to
>> bioconductor at stat.math.ethz.ch
>> In addition: Warning message:
>> In readLines(biocURL) : cannot open: HTTP status was '404 Not Found'
> 
> Hi, Radek.  Folks will probably need to see the output of
> sessionInfo() to help more.
> 
> Sean
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662