Assume that you have a count table where there are two dependent conditions with 3 replicates each.
Gene R1-C1 R2-C1 R3-C1 R1-C2 R2-C2 R3-C2 X1 43 52 38 120 131 115 X2 250 273 260 26 35 42 X3 112 100 120 205 200 150
To simulate data in a simple way, Is that correct to make an artificial count table for DE analysis by copying the first condition in the second condition like this?
Gene R1-C1 R2-C1 R3-C1 R1-C2 R2-C2 R3-C2 X1 43 52 38 43 52 38 X2 250 273 260 250 273 260 X3 112 100 120 112 100 120
So there is no DE gene. And to add some DE genes to the list, multiply some randomly chosen conditions in specified FCs.
Is that correct and acceptable?
On a paper, I read this "To assess how the different software packages and pipelines can control false positive rates, we utilized the multiple replicates within the sample groups by constructing artificial two-group comparisons. No significant detections were expected in such mock comparisons."
I just thought they had copied replicates the way I illustrated above. So that's why I'm asking you.