I am trying to find an example where an RNA-sequencing dataset was analyzed in one manner that lead to a poor false-positive rate estimation, and then analyzed in another manner that lead to a good false-positive rate estimation. Ideally, both analysis methods led to DEGs: Only in the first case, these DEGs are not as trust-worthy as in the second case because of the lower false-positive rate estimation.
I am not concerned about what package was used for the analysis or what type of RNA-sequencing dataset.
In case this is a strange question to ask... I am hoping to examine visually what DEGs "look like" when they come from an analysis that has a poor false-positive rate estimation versus a good false-positive rate estimation.
If anyone is aware of any such example code that could produce such items, I would be very grateful to be pointed in that direction! Thank you.