During the analysis of the company's transcriptome, I got a comparison of treatment vs control, but in research papers, we have to write control vs treatment. So, is it okay to rewrite it as control vs treatment, or should I have to do the analysis again?

Answer 1

You don't need to redo the analysis just to reverse the comparison order from "treatment vs control" to "control vs treatment." The results of your analysis remain valid regardless of the order in which you present the comparisons. Here’s what you can do:

Rewriting for Consistency: When writing your research paper, you can present the findings as "control vs treatment." This involves reversing the labels in your descriptions and ensuring that any statistical results, such as fold changes and p-values, are correctly interpreted in the new context.

Clarify the Direction: Clearly state in the methods section how the analysis was conducted and that you are presenting the results in the "control vs treatment" format for consistency with the literature.

Interpret Results Correctly: Be mindful of how the direction of change is reported. For example, if a gene is upregulated in treatment compared to control, it would be downregulated in the control compared to treatment, and vice versa.

Here's an example of how you might describe this in your methods section:

"For consistency with standard reporting in the literature, we present our differential expression results in the 'control vs treatment' format. The original analysis was performed as 'treatment vs control', and results have been inverted accordingly."