Question: CDF file
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gravatar for Jay an
11.7 years ago by
Jay an60
Jay an60 wrote:
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ADD COMMENTlink modified 11.7 years ago by Celine Carret220 • written 11.7 years ago by Jay an60
Answer: CDF file
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gravatar for Celine Carret
11.7 years ago by
Celine Carret220
Celine Carret220 wrote:
Hi, by googling the array name, I found this: http://inn.weizmann.ac.il/bioconductor/packages/1.9/data/annotation/ht ml /hsex10stv2hsug.html Isn't it your answer? Best wishes Celine -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jay an Sent: 06 December 2007 13:04 To: bioconductor at stat.math.ethz.ch Subject: [BioC] CDF file hello there, R could not find huex10stv2cdf and huex10stv2probe in bioconductor repository. where can I get the two files? Thanks Jay here is the error message: > normalized<-justGCRMA() Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment huex10stv2cdf was not found in the Bioconductor repository." [1] "Checking to see if your internet connection works..." [1] "Environment huex10stv2probe was not found in the Bioconductor repository." Error in get(probepackagename) : variable "huex10stv2probe" was not found > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_M ON ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.12 52 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] gcrma_2.10.0 matchprobes_1.10.0 affy_1.16.0 preprocessCore_1.0.0 [5] affyio_1.6.1 Biobase_1.16.1 > --------------------------------- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
ADD COMMENTlink written 11.7 years ago by Celine Carret220
Hello Jay and Celine, CDFs for exon arrays are "unsupported" and a bit messy indeed. They include control and background probesets that are represented as MM or single-probe-probesets. This makes raw CDFs not useful for BioConductor, and probably that's why they are not included in the BioC metadata packages. The package versions of CDFs with BKG and control probesets removed you can find at: http://xmap.picr.man.ac.uk/cdf There are some other attempts to solve the issue, it is currently discussed also on affy-aroma list. Cheers, Michal -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Celine Carret Sent: 06 December 2007 14:03 To: Jay an; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] CDF file Hi, by googling the array name, I found this: http://inn.weizmann.ac.il/bioconductor/packages/1.9/data/annotation/ht ml /hsex10stv2hsug.html Isn't it your answer? Best wishes Celine -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jay an Sent: 06 December 2007 13:04 To: bioconductor at stat.math.ethz.ch Subject: [BioC] CDF file hello there, R could not find huex10stv2cdf and huex10stv2probe in bioconductor repository. where can I get the two files? Thanks Jay here is the error message: > normalized<-justGCRMA() Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment huex10stv2cdf was not found in the Bioconductor repository." [1] "Checking to see if your internet connection works..." [1] "Environment huex10stv2probe was not found in the Bioconductor repository." Error in get(probepackagename) : variable "huex10stv2probe" was not found > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_M ON ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.12 52 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] gcrma_2.10.0 matchprobes_1.10.0 affy_1.16.0 preprocessCore_1.0.0 [5] affyio_1.6.1 Biobase_1.16.1 > --------------------------------- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:13}}
ADD REPLYlink written 11.7 years ago by Michal Okoniewski120
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