I have a question related to the analysis of the microarray data. In the process of differential gene expression analysis, filtering low probe intensities is very crucial. The array chip I am analyzing presently is HuGene1.0 ST array. I am using oligo package in R to analyze and rma normalization method. Can anyone recommend how to filter low probe intensities and how to derive a cut-off to know that these are the probes with low intensities?
Thanks a lot.