Dear Bioconductor Community,
i have recently analyzed two different microarray datasets using the same pipeline in R. Both of the datasets have the same variables and the comparizon was cancer vs normal samples in order to find DE genes. Moreover. both of the datasets are Affymetrix platform, but different genechip: hgu133a & hgu133plus2. Finally, after annotating results from both datasets, i found in common 278 genes with same probeIDs(from topTable in limma). My question is whether it is possible and applicable in someway to combine both datasets and the expressions about these specific genes, in order to infer common patterns or similar expressions in these genes ?(for instance with heatmap). Im concerned that merging different datasets includes many pitfalls or serious batch effects, but here my goal is to test the possibility to infer any important information that can be excluded from both of these datasets regarding colon cancer ?