Question: a question about getCdfInfo package in GCRMA, thanks for your help.
0
gravatar for liuyang zhao
8.1 years ago by
liuyang zhao20
liuyang zhao20 wrote:
Dear bioconductor: I input code as follow: >library(gcrma) >mydata<-ReadAffy(widget=TRUE) >eset_gcrma<-gcrma(mydata) then showing error: wrong on getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain U133_X3Pa520049 Library - package u133x3pa520049cdf not installed Bioconductor - u133x3pa520049cdf not available Would you please tell me how to solve this problem? Thanks for your kind help. Attach is a cel file,thanks. Liuyang Zhao Chongqing Medical University
cdf • 850 views
ADD COMMENTlink modified 3.8 years ago by zhilongjia0 • written 8.1 years ago by liuyang zhao20
Answer: a question about getCdfInfo package in GCRMA, thanks for your help.
0
gravatar for James W. MacDonald
8.1 years ago by
United States
James W. MacDonald51k wrote:
Hi Liuyang Zhao , On 10/9/2011 10:47 PM, liuyang zhao wrote: > Dear bioconductor: > > > I input code as follow: > >> library(gcrma) >> mydata<-ReadAffy(widget=TRUE) >> eset_gcrma<-gcrma(mydata) > then showing error: > > wrong on getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: Specified > environment does not contain U133_X3Pa520049 Library - package > u133x3pa520049cdf not installed Bioconductor - u133x3pa520049cdf not > available This doesn't appear to be a commercially available chip, so you will need to create a cdf package yourself, using the makecdfenv package. Please see the vignette for that package. library(makecdfenv) vignette("makecdfenv") Best, Jim > > > Would you please tell me how to solve this problem? > > Thanks for your kind help. > > > Attach is a cel file,thanks. > > > Liuyang Zhao > > Chongqing Medical University > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues [[alternative HTML version deleted]]
ADD COMMENTlink written 8.1 years ago by James W. MacDonald51k
Answer: a question about getCdfInfo package in GCRMA, thanks for your help.
0
gravatar for zhilongjia
3.8 years ago by
zhilongjia0
United Kingdom
zhilongjia0 wrote:

Adding mydata@cdfName <- "U133_X3P"

before eset_gcrma<-gcrma(mydata) will work.

ADD COMMENTlink written 3.8 years ago by zhilongjia0
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