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 I can 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)