Can't use package [pd.mapping250k.sty]
1
0
Entering edit mode
@marcelo-pereira-6541
Last seen 8.0 years ago
Hello, I have been trying to use the package *[pd.mapping250k.sty]*, but I’m might be missing something. This is my procedure: > myData <- ReadAffy() > myData@cdfName [1] "Mapping250K_Sty" The CEL fled are loaded okay!! Then we proceed with the normalization procedure, and this is where the problem is: > eset <- rma(myData) *Error in getCdfInfo(object) :* * Could not obtain CDF environment, problems encountered: Specified environment does not contain Mapping250K_Sty* *Library - package mapping250kstycdf not installed* *Bioconductor - mapping250kstycdf not available* Then, I tried installing it: > biocLite(‘pd.mapping250k.sty’) > library(‘pd.mapping250k.sty’) The package installs okay (it is a ~350Mb package), and it DOES load properly, but when I tried to run rma(myData) again I get the same problem as above: *Error in getCdfInfo(object) :* * Could not obtain CDF environment, problems encountered: Specified environment does not contain Mapping250K_Sty* *Library - package mapping250kstycdf not installed* *Bioconductor - mapping250kstycdf not available* I CAN rma normalize other CEL files using hgu133plus2cdf, or hgu133acdf, but NOT with Mapping250K_Sty. Any suggestions? Thanks, Marcelo [[alternative HTML version deleted]]
cdf cdf • 1.2k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 minute ago
United States
Hi Marcelo, For SNP chips of that type, you want to use the oligo package, and the crlmm function. Best, Jim On Aug 8, 2014 3:23 PM, "Marcelo Pereira" <marcelops@gmail.com> wrote: > Hello, > > I have been trying to use the package *[pd.mapping250k.sty]*, but I’m might > be missing something. > > This is my procedure: > > > myData <- ReadAffy() > > myData@cdfName > > [1] "Mapping250K_Sty" > > > The CEL fled are loaded okay!! Then we proceed with the normalization > procedure, and this is where the problem is: > > > eset <- rma(myData) > > *Error in getCdfInfo(object) :* > * Could not obtain CDF environment, problems encountered: Specified > environment does not contain Mapping250K_Sty* > *Library - package mapping250kstycdf not installed* > *Bioconductor - mapping250kstycdf not available* > > > Then, I tried installing it: > > > biocLite(‘pd.mapping250k.sty’) > > library(‘pd.mapping250k.sty’) > > The package installs okay (it is a ~350Mb package), and it DOES load > properly, but when I tried to run rma(myData) again I get the same problem > as above: > > *Error in getCdfInfo(object) :* > * Could not obtain CDF environment, problems encountered: > Specified environment does not contain Mapping250K_Sty* > *Library - package mapping250kstycdf not installed* > *Bioconductor - mapping250kstycdf not available* > > > I CAN rma normalize other CEL files using hgu133plus2cdf, or hgu133acdf, > but NOT with Mapping250K_Sty. > > Any suggestions? > > Thanks, > Marcelo > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
ADD COMMENT

Login before adding your answer.

Traffic: 735 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6