Hello I have an ExpressionSet object that I would like to save it to csv file. My question is how to transpose it to have the genes names on the rows and the columns name on the columns. Also how to save it with columns and rows headers? Below is the code.

library(Biobase) library(genefilter) library(data.table)

phenoData:

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

featureData:

tmp <- read.csv("fdata.csv", 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)

f1 <- kOverA(5, 800) ffun <- filterfun(f1) wh1 <- genefilter(exprs(eset), ffun) eset=eset[wh1] write.csv( eset, file = "cleanData.csv", col.names=TRUE)

You can transpose the data frame and then save it, like this:

tmp <- t(tmp) #transpose data frame

write.csv(tmp, "tmp.csv", row.names = TRUE, col.names = TRUE) # make sure to set row.names to TRUE!

Why are you going to all the trouble of creating an ExpressionSet, which is intended as an object to be used within R, just to output the data? That seems to be lots of work for no gain. Do note that kOverA requires that you extract the data from your ExpressionSet, so you are creating an ExpressionSet in order to extract something from it and then write that back out.

In addition, by default the expectation for genomic data in Bioconductor is to have the genes in rows and samples in columns, so if that's not how your data are already set up, then you are not using kOverA as intended. As for saving it with column and row headers, have you read the help page for write.table?