I am trying to replicate the results of a paper. I have done all the necessary steps to find the differentially expressed genes using limma package in R. But contrary to the results presented in the paper, most of the significantly expressed genes (90%) are downregulated. Only 3 genes are upregulated. Is there a reason for this?
Did you try running the script they provided?
The paper description of the analysis is very general, and you don't show anything about the analysis you have done. It would be difficult to replicate their analysis due to the lack of details (such as versions of the software used, particular parameters used, and so on), and it is difficult to speculate why your analysis differ from theirs, as both analyses are largely unknown.
As h.mon said, without more information it's impossible to know what's causing these differences.
To hazard a guess, did you flip comparison? The paper shows 12 upregulated and 4 downregulated genes. If you're seeing 27 downregulated and 3 upregulated genes you could have the denominator and numerator flipped in your comparison.