Hai, I am using the data obtained from Agilent 8x60k chip for the analysis of mRNA expression. I have gone through lots of papers that describes only about Agi 4x44 chips. Here am facing a trouble of filtering the genes using the LIMMA package in R+Bioconductor. What is the basic code implemented in doing this filtering process? I just want to know how the unwanted ProbeID,s or genes, which are of not importance, can be filtered out using the LIMMA package. The code for normalization that i am using is: *y <- normalizeBetweenArrays(y, method="quantile")* * * * * Could you please help me by providing the code that can be used for the filtering of 8x60k data using LIMMA package in R+Bioconductor? [[alternative HTML version deleted]]