I am trying to explore differential expressions of a selected cluster between two sample groups. However, it showed warning “For the selected comparison, there are fewer than 3 samples with the minimum number of cells (10). Only logFC values will be calculated and results should be used for exploratory purposes only.” Is there a way to solve this problem?
Thanks for your question!
The most likely explanation for this warning when performing differential expression is that you are comparing 1 sample to 1 other sample. When you perform a 1 vs 1 comparison like this, the Differential Expression results will show the LogFC difference but the results will not show an adj p-value. The reason for this is that it is not statistically sound to calculate the p-value when comparing 1 vs 1. However, the differential expression comparison can still be performed and the LogFC will be returned.
You asked how to solve this ‘problem’. The way to address this warning is to increase N in your differential expression comparison e.g. to instead compare groups with multiple samples so that there are more than 3 samples in total (such as 1 vs 2, or 2 vs 2).
I hope this makes sense! Let me know if you have further questions.