Dear community,
I found that a gene that has only a small fold-change between two conditions based on MAST, conversely appears to have a large difference if plotted in a dotplot:
MAST results:
gene log2FC pct.1 pct.2
Flt1 -0.02 0.98 0.99
The effect size is not huge, but in the dotplot the difference looks even stronger that that of the MAST top hit (which has a 50-fold smaller pvalue).
Unscaled normalized values were used for MAST.
Please note that the gene is highly expressed. Maybe that has an effect on MAST?
Any advice is appreciated!