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

[Radek Blatny]

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.U 
TF-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_ID 
ENTIFICATION=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