Hi,

Is it possible to create an expression set from 1. a text file containing an the results of an RMA normalization 2. a csv file containing the annotation for the specific affy chip pertaining to the normalized data. If yes please advise.

Thanks.

It is possible to construct an ExpressionSet from separate files. For example imagine you have three separate files, one for the expression data (e.g. from RMA as you mentioned), another with probe annotations (like your csv one) and another with sample annotations. For example:

#===========================
# phenoData - sample annotations.
# pdata.txt (comma separated)
# 
# id,treatment
# sample1,1
# sample2,1
# sample3,0
# sample4,0

#===========================
# featureData - probe annotations.
# fdata.txt (comma separated)
# 
# id,symbol
# probe1,gene1
# probe2,gene2
# probe3,gene3
# probe4,gene4

#===========================
# expression data
# 
# exprs.txt (tab delimited)
# sample1 sample2 sample3 sample4
# probe1 10 9 11 8
# probe2 10 11 2 1
# probe3 2 3 12 10
# probe4 1 3 2 1

I assumed the annotations to be comma separated value files and the expression data to be tab separated file. But this does not matter- it only changes the R function used to read it. You can do then something like this:

library(Biobase)

# phenoData:
tmp <- read.csv("pdata.txt", row.names = 1)
pdata <- AnnotatedDataFrame(tmp)

# featureData:
tmp <- read.csv("fdata.txt", row.names = 1)
fdata <- AnnotatedDataFrame(tmp)

# expression data:
tmp <- read.table("exprs.txt")
m <- as.matrix(tmp)

## create ExpressionSet object:
eset <- new("ExpressionSet", exprs = m, phenoData = pdata, featureData = fdata)

pData(eset)
fData(eset)
eset$treatment

The only requirement (I think) is that the sample names and feature names agree between the different files.

Dear Vani,

suppose for the first case of the txt file, the file has headers with the sample names and the rows are the probesets.

You can use then in your current directory:

rma.file <- read.table("name of your file.txt", header=TRUE, sep="\t") # the last argument not neseccary

eset <- new("ExpressionSet", exprs=as.matrix(rma.file))

In similar way, you can use read,csv for the csv file . You can check also in more detail the above functions, including read.delim