I have a matrix of gene expression which label of each sample and symbol of each gene is known. I wanna perform gtBroad in globaltest R-package. It needs to convert expression matrix to an ExpressionSet object with known Annotation. How can I do that while I have only the name of genes?

EDIT: You can download sample data from this link: https://www.dropbox.com/s/d50tr958yvvcxwx/TEST.Rdata?dl=0

I wanna run the below code:

library(globaltest)
library(GSEABase)
broadset <- getBroadSets(asBroadUri(c('BIOCARTA_HDAC_PATHWAY', 'PID_HDAC_CLASSII_PATHWAY')))
pData <- data.frame(id=resp, row.names=colnames(data))
phenoData <- AnnotatedDataFrame(data=pData)
exprs <- ExpressionSet(data, phenoData=phenoData)
gtBroad (response=id, exprs, id='PID_HDAC_CLASSIII_PATHWAY', collection=broadset)

Making an expression set object is straight forward. You will need the gene expression data in matrix format with gene names as row names. You will then need an annotation data frame with the sample names as row names (these are column names in the matrix). I have my example below.

data <- as.matrix(data)
row.names(des) <- des$ID
des_ready <- as(des, "AnnotatedDataFrame")
x <- ExpressionSet(data, phenoData=des_ready)

http://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/Biobase/html/class.ExpressionSet.html