[BioC] ai<-compute.affinities(mm430mmentrezg7)
Radek Blatny
blatny at img.cas.cz
Tue Aug 12 18:14:14 CEST 2008
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.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
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