Entering edit mode
Sally -- I saw your earlier post and wanted to help, but your example
is too long for me to work with, and I couldn't run it myself (I don't
have your data!). Plus I couldn't see where in your original post the
mistake was occurring, and below you don't have sessionInfo so you
could be using some hodge-podge of packages that weren't designed to
work together anyway..
I was going to suggest that you trim your example down to something
small and reproducible. In thinking about how you might do that, I
looked at where the error occurs
> fit2 <- eBayes(fit2)
> write.table(fit2,file="fit2.txt",sep="\t")
and a possibility hit me. Here's my thought process -- what is the
class of fit2? what types of argument does write.table accept? in
what package is the class of fit2 defined? is there another function
in the package where the class of fit2 is defined that might be what
you were looking for?
Hope that helps,
Martin
"Sally" <sagoldes at="" shaw.ca=""> writes:
> I have the following code, from which I get the following error
message:
>
> Error in dim(data) <- dim : attempt to set an attribute on NULL
>
> The script works fine until I get to the ------ line below at the
end of the data.
>
> #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=T
RUE,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=
"Galfile.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")
>
> --------------------------------------------------------------------
-----------------------------------------------
>
>>From here on-down it does not work
>
> #I took the fit2 table and manually removed all empty and GFP rows,
plus I deleted all rows where the Fpval was greated than 0.01. This
table is called
> #fit2readformulttestFp01.txt
>
>
> fit2<-read.table("fit2readyformulttestFp01.txt", header=TRUE,
sep="\t") #WORKS
> write.table(fit2, file="filteredfit2.txt", sep="\t") #WORKS
>
>
> s0vss24<-topTable(fit2,coef="s0vss24",number=3412,adjust.method="BH"
,p.value=1)
>
> write.table(s0vss24,file="s0vss24.txt",sep="\t")
>
>
> s24vss48<-topTable(fit2,coef="s24vss48",number=3412,adjust.method="B
H",p.value=1)
>
> write.table(s24vss48,file="s24vss48.txt",sep="\t")
>
>
> s48vss96<-topTable(fit2,coef="s48vss96",number=3412,adjust.method="B
H",p.value=1)
>
> write.table(s48vss96,file="s48vss96.txt",sep="\t")
>
>
> c0vsc24<-topTable(fit2,coef="c0vsc24",number=3412,adjust.method="BH"
,p.value=1)
>
> write.table(c0vsc24,file="c0vsc24.txt",sep="\t")
>
>
> c24vsc48<-topTable(fit2,coef="c24vsc48",number=3412,adjust.method="B
H",p.value=1)
>
> write.table(c24vsc48,file="c24vsc48.txt",sep="\t")
>
>
> c48vsc96<-topTable(fit2,coef="c48vsc96",number=3412,adjust.method="B
H",p.value=1)
>
> write.table(c48vsc96,file="c48vsc96.txt",sep="\t")
>
> Thanks, .../Sally
>
> [[alternative HTML version deleted]]
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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