can some please suggest me about the following problem and solution to this.I am not so familiar to gene expression studies,
Q. I have an gene expression data set containing more than 16,000 probes (whole data) after normalization and filtering.
A subset of these probes (4,000 Probes) were independently considered for E Bayes test. I performed DE analysis to both set containing whole data (16, 000 Probes) and subset data(4,000 Probes).
When I compared both the dataset after DE analysis based on adj.p.value , Some Probes which are differentially expressed in the subset data were not found in the whole data. I would expect the same probes which are DE in the subset should be there in Whole data. It would be great if i get to know whether my assumption is wrong ?