Just a discussion,
For microArray data, there are always two ways to obtain the expression value for probe across the samples,
1) download the original CEL files, then use ReadAffy & rma to get the matrix OR use justRMA directly
2) use GEOquery to obtain the matrix directly
However, I found somehow minimal difference between these two method, but I do not know why?
Another question is that can I use the matrix from GEOquery to directly do differential expression analysis as outputs of rma?
And which one is better for DE analysis, 1) using probe level 2) using gene level Because one gene may point to several probes, when we carry out DE analysi, one step is to obtain the DE output which needs p.adjust, so the question is that the array may have 50K probes but only have 20k genes, which may results quite different results.
Anyone can answer these questions?