I am getting the following error message: Error in dim(data) <- dim : attempt to set an attribute on NULL from the following Limma script (post-pre-processing) #Load libraries source("http://bioconductor.org/biocLite.R") biocLite() library(limma) library(Biobase) #change directory to folder where files are (c:/limmadegenes) #Change to directory with original data files #read in expression data file and phenotypic data. #Note that row.names=1 means that row names are #in column 1, exprdata<-read.table("exprsData.txt", header=TRUE,sep="\t",row.names=1,as.is=TRUE,fill=TRUE,) class(exprdata) #[1] "data.frame" dim(exprdata) #[1] 17328 28 colnames(exprdata) head(exprdata) #printout too long to paste phenotypicdata<-read.table("phenotypicdata.txt",row.names=1,header=TRU E,sep="\t") class(phenotypicdata) #returns: [1] "data.frame" dim(phenotypicdata) #returns: [1] 28 2 colnames(phenotypicdata) #returns: [1] "Species" "Time" rownames(phenotypicdata) #Coerse exprdata into a matrix myexprdata<-as.matrix(exprdata) write.table(myexprdata,file="myexprdata.txt",sep="\t",col.names=NA) class(myexprdata) #[1] "matrix" rownames(myexprdata) colnames(myexprdata) #Coerse phenotypicdata into a data frame myphenotypicdata<-as.data.frame(phenotypicdata) write.table(myphenotypicdata,file="myphenotypicdatacheck.txt",sep="\t" ,col.names=NA) rownames(myphenotypicdata) colnames(myphenotypicdata) #[1] "species" "time" summary(myphenotypicdata) all(rownames(myphenotypicdata)==colnames(myexprdata)) #[1] TRUE #Create annotated Data Frame adf<-new("AnnotatedDataFrame",data=phenotypicdata) #dim means: dimension of an object. dim(adf) #rowNames columnNames # 28 2 rownames(adf) #NULL #read in galfile readGAL("Galfile.gal") #Create eset object eSet<-new("ExpressionSet",exprs=myexprdata,phenoData=adf,annotation="G alfile.gal") #Read in targets file targets <- readTargets("targets.txt") targets # Set up character list defining your arrays, include replicates TS <- paste(targets$Species, targets$Time, sep=".") #This script returns the following: TS # Turn TS into a factor variable which facilitates fitting TS <- factor(TS) #This script returns the following design <- model.matrix(~0+TS) #write design object to text file write.table(design,file="design.txt",sep="\t",col.names=NA) colnames(design) <- levels(TS) #for eset put in your M values - see ?lmFit for object types fit <- lmFit(eSet, design) cont.matrix<-makeContrasts(s0vss24=s.0-s.24, s24vss48=s.24-s.48, s48vss96=s.48-s.96, c0vsc24=c.0-c.24, c24vsc48=c.24-c.48, c48vsc96=c.48-c.96, levels=design) write.table(cont.matrix,file="cont.matrix.txt",sep="\t",col.names=NA) # estimate the contrasts and put in fit2 fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) #print fit2 table write.table(fit2,file="fit2.txt",sep="\t") #Filtering: I took the fit2 table and removed all empty and GFP spots, plus I deleted all rows where the Fpval was greated than 0.01. This table is called #fit2readformulttestFp01.txt filteredfit2<-read.table("fit2readyformulttestFp01.txt", header=TRUE, sep="\t") write.table(filteredfit2, file="filteredfit2.txt", sep="\t") fit3<-as.data.frame(filteredfit2,row.names=NULL) class(fit3) #returns data.frame write.table(fit3, file="fit3.txt",sep="\t") s0vss24<-topTable(fit3,coef="s0vss24",number=3412,adjust.method="BH",p .value=1) write.table(s0vss24,file="s0vss24.txt",sep="\t") s24vss48<-topTable(fit3,coef="s24vss48",number=3412,adjust.method="BH" ,p.value=1) write.table(s24vss48,file="s24vss48.txt",sep="\t") s48vss96<-topTable(fit3,coef="s48vss96",number=3412,adjust.method="BH" ,p.value=1) write.table(s48vss96,file="s48vss96.txt",sep="\t") c0vsc24<-topTable(fit3,coef="c0vsc24",number=3412,adjust.method="BH",p .value=1) write.table(c0vsc24,file="c0vsc24.txt",sep="\t") c24vsc48<-topTable(fit3,coef="c24vsc48",number=3412,adjust.method="BH" ,p.value=1) write.table(c24vsc48,file="c24vsc48.txt",sep="\t") c48vsc96<-topTable(fit3,coef="c48vsc96",number=3412,adjust.method="BH" ,p.value=1) write.table(c48vsc96,file="c48vsc96.txt",sep="\t") ALSO: What does this error message mean? In addition: Warning messages: 1: In safeSource() : Redefining 'biocinstall' 2: In safeSource() : Redefining 'biocinstallPkgGroups' 3: In safeSource() : Redefining 'biocinstallRepos' [[alternative HTML version deleted]]