Hello, I try through affycomp different methods with one another compare. I have step by step instructions of http://affycomp.biostat.jhsph.edu/#whatisthis used: >>Data and instructions >>Download the spike-in and dilution data sets. >>Spike-in hgu133a Data >>Affymetrix's Spike-in hgu133a Experiment CEL files [gzip-compressed tar-archive] >>Description file for this data [text] ::: I downloaded. >>2. Obtain expression measures (in original scale, NOT log scale) for any or all of the datasets, and write each as a comma-delimited text file as follows: >>For R users, if x is matrix with probe set IDs as rownames and filenames as colnames, the command write.table(data.frame(x,check.name s=FALSE),file="filename.csv",sep=",",col.names=NA,quote=FALSE) should do the trick. >>For convenience, we offer two example files [compressed archive] in the correct format, one for dilution and one for spike-in. ::: Iwrote: library(affy) library(affycomp) data.raw <- ReadAffy(filenames="./R/ME_cel/Expt1_R1.CEL", ... "./R/ME_cel/Expt7_R2.CEL") eset <- mas5(data.raw) :::For data.frame I receive error message: #write.table(eset(x,check.names=FALSE),file="filename.csv",sep=",",col .names=NA,quote=FALSE) #Error in inherits(x, "data.frame") : couldn't find function "eset" ::: I can the following commands use, but csv file is not stored like given examples: write.table(eset,file="filename.csv",sep=",",col.names=NA,quote=FALSE) How can I produce correct data.frame? Thanks, Mohammad Esad-Djou

Thanks for your answer. I have the following questions: 1. How can I produce data.frame correct without Preprocessing (MAS5, RMA, liwong...)? I know that the instruction is not correct: data.raw <- ReadAffy(filenames="./R/ME_cel/Expt1_R1.CEL", ... "./R/ME_cel/Expt7_R2.CEL") x<- exprs(data.raw) but I have unfortunately no new Idea! 2. (in affycomp) Can I use directly *.CEL files instead of *.csv? If yes, how? Thanks, Mohmmad Esad-Djou "Rafael A. Irizarry" <ririzarr@jhsph.edu> schrieb am 18.05.05 20:35:36: > > the instructions say you should do this: > > x <- exprs(eset) > write.table(data.frame(x,check.names=FALSE),file="filename.csv",sep= ",",col.names=NA,quote=FALSE) > > > -r > > On Wed, 18 > May 2005, Mohammad Esad-Djou wrote: > > > Hello, > > > > I try through affycomp different methods with one another compare. > > > > I have step by step instructions of http://affycomp.biostat.jhsph.edu/#whatisthis used: > > > > >>Data and instructions > > >>Download the spike-in and dilution data sets. > > > > >>Spike-in hgu133a Data > > >>Affymetrix's Spike-in hgu133a Experiment CEL files [gzip- compressed tar-archive] > > > > >>Description file for this data [text] > > > > ::: I downloaded. > > > > >>2. Obtain expression measures (in original scale, NOT log scale) for any or all of the datasets, and write each as a comma-delimited text file as follows: > > >>For R users, if x is matrix with probe set IDs as rownames and filenames as colnames, the command write.table(data.frame(x,check.name s=FALSE),file="filename.csv",sep=",",col.names=NA,quote=FALSE) should do the trick. > > >>For convenience, we offer two example files [compressed archive] in the correct format, one for dilution and one for spike-in. > > > > ::: Iwrote: > > > > library(affy) > > library(affycomp) > > > > data.raw <- ReadAffy(filenames="./R/ME_cel/Expt1_R1.CEL", > > ... > > "./R/ME_cel/Expt7_R2.CEL") > > > > eset <- mas5(data.raw) > > > > :::For data.frame I receive error message: > > #write.table(eset(x,check.names=FALSE),file="filename.csv",sep="," ,col.names=NA,quote=FALSE) > > #Error in inherits(x, "data.frame") : couldn't find function "eset" > > > > ::: I can the following commands use, but csv file is not stored like given examples: > > write.table(eset,file="filename.csv",sep=",",col.names=NA,quote=FALSE) > > > > How can I produce correct data.frame? > > > > Thanks, > > Mohammad Esad-Djou > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >