i would like to ask you a more "beginner" question about a initial comparison of DE lists i have acquired from limma, between two microarray datasets. Although the platform is the same (Agilent), the comparisons are somehow-different due to the different time point of comparison: in the one dataset, i have compared bystander samples vs controls in 4hours, whereas in the other i have performed the same comparison, but in the time-point of 30 min. Also, the same cell type was used in both experiments--IMR-90 human lung fibroblasts--. I understand due to the different time-point comparison, any general comparisons might be inappropriate-but, as I'm highly interested of finding common DE genes between both time-points--which could indicate interesting patterns or groups of genes in both time-points:
thus, for a start, i could compare the DE probe-sets (i.e. with adjusted p-val < 0.05) in a VENN diagram ? or i could also compare the final gene symbols, in case i miss anything for different DE probe-sets in the two datasets, annotated in the same gene symbol ?
Finally, also a scatter-plot would be helpful for this cause ? And if my notion is correct, i should similarly use the logFCs or the t-statistics from the common probe-sets/gene symbols ?