So I have a simple question. Suppose I download 2 or more dataset from NCBI GEO. Those dataset come from different experiment especially the NGS machine. For example one of them use Illumina and others use Ion Torrent.
My first question is, if I calculated each dataset separately for DEG, using EdgeR, Limma/Voom, or DEseq2, are these log fold change comparable?
For example, Dataset 1 comes from Illumina Hiseq and I have logfoldchange from DESeq2. ANother Dataset 2 comes from IonTorrent and I have logfoldchange from DESeq2.
My second question is, what if I calculate the DEG using different method? One of them using DESeq2 and other use Limma/voom?
What should I consider?