Question: Problem in running expresso command in affy package
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gravatar for Priyanka Jain
9.6 years ago by
Priyanka Jain20 wrote:
Hello, I am using affy package of Biconductor.I have given raw cel files as input for normalization. I have to do background correction and normalization of these files. I am using the following commands: > library(affy) > Data<-ReadAffy() > est<-rma(Data) Background correcting Normalizing Calculating Expression Warning message: package 'hgu133acdf' was built under R version c(2, 0, 0) and help will not work correctly Please re-install it S4' > write.exprs(est,file="backgroud_corrected") Till here the raw cel file is being background corrected without any error. But when i am using expresso command >normalized<-expresso(Data,normalize.method="qspline",bgcorrect.method ="rma",pmcorrect.method="pmonly",summary.method="liwong") > write.exprs(normalize, file="normalize_using_expresso") using expresso command the file is not being normalized. Please try to solve this problem as early as possible. With Regards, Priyanka Jain [[alternative HTML version deleted]]
normalization affy • 739 views
ADD COMMENTlink modified 9.6 years ago by Seth Falcon7.4k • written 9.6 years ago by Priyanka Jain20
Answer: Problem in running expresso command in affy package
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gravatar for Seth Falcon
9.6 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Hi, Please read the posting guide and provide the list with more information about your setup (sessionInfo()) as well as more details on what isn't working. Ideally, try to provide an easily reproducible example perhaps using sample data that comes with the packages. + seth On 3/27/10 1:00 AM, Priyanka Jain wrote: > Hello, > > I am using affy package of Biconductor.I have given raw cel files > as input for normalization. I have to do background correction and > normalization of these files. > > I am using the following commands: > >> library(affy) >> Data<-ReadAffy() >> est<-rma(Data) > Background correcting > Normalizing > Calculating Expression > Warning message: > package 'hgu133acdf' was built under R version c(2, 0, 0) and help will not > work correctly > Please re-install it > S4' >> write.exprs(est,file="backgroud_corrected") > > Till here the raw cel file is being background corrected without any error. > > But when i am using expresso command > >> normalized<-expresso(Data,normalize.method="qspline",bgcorrect.meth od="rma",pmcorrect.method="pmonly",summary.method="liwong") >> write.exprs(normalize, file="normalize_using_expresso") > > > using expresso command the file is not being normalized. > > Please try to solve this problem as early as possible. > > > With Regards, > Priyanka Jain > > [[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 -- Seth Falcon Bioconductor Core Team | FHCRC
ADD COMMENTlink written 9.6 years ago by Seth Falcon7.4k
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