Can Bioconductor be used offline?
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Fedor Syagin ▴ 10
@fedor-syagin-5670
Last seen 7.1 years ago
Greetings. Sorry to bother you. My name is Fedor Syagin and I work for Columbia University - C2B2. One of the users on our computational cluster keep getting following error Adjusting for optical effect................................................................ .... ...................................................................... .... ...................................................................... .... ...................................................................... .... ...................................................................... .... ...................................................................... .... ...................................................................... .... ...................................................................... .... ...................................................................... .... ...................................................................... .... ...................................................................... .... ........................................................Done. Computing affinitiesError in getProbePackage(probepackagename) : The current operation could not access the Bioconductor repository. Please check your internet connection, and report further problems to bioconductor@stat.math.ethz.ch Calls: gcrma ... bg.adjust.gcrma -> compute.affinities -> getProbePackage after running following code: library ("AnnotationDbi") library("affy") library("affyPLM") library("simpleaffy") library("yaqcaffy") library("gcrma") library("limma") library("arrayQualityMetrics") library("gplots") AffyBatch = ReadAffy() NormalizedEset_gcrma <- gcrma(AffyBatch,fast=FALSE) When job are submitted on the cluster there is no internet connectivity - so question is does this error indicate that Bioconductor require active internet connection at all time (not only during package installation) or this is error in code / installation. Is there a particular way how this can be avoided that comes to your mind. I would appreciate your help in this matter. Thank you and have great holidays. Sincerely yours Fedor Syagin (212) 851-4796 (917) 710-6664 [[alternative HTML version deleted]]
gcrma gcrma • 743 views
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@wolfgang-huber-3550
Last seen 11 weeks ago
EMBL European Molecular Biology Laborat…
Dear Fedor it should be sufficient to install the 'probe' package associated with your microarray type. http://www.bioconductor.org/packages/release/BiocViews.html#___Affymet rixChip Best wishes Wolfgang Il giorno Dec 21, 2012, alle ore 10:06 PM, Fedor Syagin <fs2307 at="" c2b2.columbia.edu=""> ha scritto: > Greetings. > > Sorry to bother you. > > My name is Fedor Syagin and I work for Columbia University - C2B2. > > One of the users on our computational cluster keep getting following error > > > Adjusting for optical > effect.............................................................. ...... > .................................................................... ...... > .................................................................... ...... > .................................................................... ...... > .................................................................... ...... > .................................................................... ...... > .................................................................... ...... > .................................................................... ...... > .................................................................... ...... > .................................................................... ...... > .................................................................... ...... > ........................................................Done. > Computing affinitiesError in getProbePackage(probepackagename) : > 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 > Calls: gcrma ... bg.adjust.gcrma -> compute.affinities -> getProbePackage > > > > > > after running following code: > > > > library ("AnnotationDbi") > > library("affy") > > library("affyPLM") > > library("simpleaffy") > > library("yaqcaffy") > > library("gcrma") > > library("limma") > > library("arrayQualityMetrics") > > library("gplots") > > > > AffyBatch = ReadAffy() > > NormalizedEset_gcrma <- gcrma(AffyBatch,fast=FALSE) > > > > > > When job are submitted on the cluster there is no internet connectivity - > so question is does this error indicate that > > Bioconductor require active internet connection at all time (not only > during package installation) or this is error in code / installation. > > > > Is there a particular way how this can be avoided that comes to your mind. > > I would appreciate your help in this matter. > > Thank you and have great holidays. > > > > > > Sincerely yours Fedor Syagin > > > > (212) 851-4796 > > (917) 710-6664 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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