Hello there, I am a beginner, Now I initially know how to use "affy" package and "limma" package to find Affymetrix chip differentially expressed genes. But I do not know how to use the "marray" package to analyze Agilent chips, or how to use the lumi package to analyze "Illumina" chips. Although I have read the instructions for both packages and downloaded the data from GEO, I still do not know how to build a differential expression matrix step by step. Sincerely hope that your answer.