I have annotated the .cel files and got the log2 transformation values of 12 gastric effected patients and 15 normal (control) samples patients data and 54675 probes. I want to find DEGs from the log2 transformation values with limma package.
library(affy) library(affyQCReport) library(limma) library(tkWidgets) library(oligo) list.celfiles() names=list.celfiles() names=dir(pattern = "CEL.gz") #reading celfiles from oligo package array = read.celfiles(names) #converts an AffyBatch object into an ExpressionSet object using the robust multi-array average (RMA) expression measure. eset = rma(array) # Finally, save the data to an output file to be used by other programs, etc (Data will be log2 transformed and normalized) write.exprs(eset, file="array.txt") #Read CEL files into an Affybatch. array = ReadAffy(widget=TRUE) library(affyQCReport) affyQAReport(array) arrayaffy = read.table("array.txt", header = TRUE, sep="", row.names=1) library(limma) targets <- readTargets("array.txt") targets
How do I approach from then on? Thank you in advance