What are the differences between pair-wise comparisons and time-series comparisons?

  • A pair-wise comparison tests for genes that are differentially expressed between any pair of groups. For example, take three groups A, B, and C. The “all pairwise” comparison will contrast A-B, A-C, and B-C.

  • Time-series are commonly used when gene expression was measured at multiple time points, or after treatments with varying concentrations/durations. A time-series comparison will only contrast consecutive pairs of groups, so in our example with three time points (A, B, C), only A-B and B-C will be performed

There is something wrong with the “Pairwise comparisons”. It does not return the right results now. The returned results seem to be the results of all “specific comparisons”. Please check this function. Thank you!

Hello Zwedan,

What do you mean exactly by that? Can you elaborate?


Hi, Guangyan. Thanks for your timely reply. I retried the “Pairwise comparison” today. And it output a collection of comparison results between each pair of all the groups, which is same with the results of “specific comparisons”. I have used the “Pairwise comparison” function previously. It output a single list table, which is different from the results nowadays. You may try the “Specific comparisons” and “Pairwise comparison”.

Hello Zwdan,

Which algorithm was it? I know I fixed a bug for DESeq2, the previous results was a single table but I revisited the code it was incorrect.


Dear Guangyan,
I do not know the algorithm. And I just find the differences between the current and previous results of the “Pairwise comparisons”. I think you may need to confirm that the results of the current “Pairwise comparisons” is correct. Thanks for your help!