Sample Information: 8 groups of cells (cell1,cell2,cell3,cell4,cell5,cell6,cell7,cell8), 4 replicates each group, 32 samples in total.
Comparison we are interested in: cell1-vs-cell2, cell3-vs-cell4,cell5-vs-cell6,cell7-vs-cell8
*Pay attention: sample 1,2 and sample 3,4 in each sample are sequenced in different platform, in an order word, there are batch effect in the samples
I analysed the data twice, with the same operation but with different input. First, I inputed all the data of 32 samples. In the second analysis, I inputed the data only with cell7 and cell8 (8 samples in total). I want to get DEGs of cell7-vs-cell8. In the first time, I got 266 DEGs, while I got none in the second time. It confused me a lot, it shouldn't be the result like that.
I hope someone would offer me some ideas. From all of my heart, sincerely.