How can I take cell number into account to find total RNA expression?

To me, it looks like the widest parts of the plots are higher in the treated. I don't see why you are so sure that the violin plots are hugely different from the calculated averages.

Either way, the differences are really small. Maybe not statistically significant.

BTW, in the future, you might want to disguise your treatment and gene of interest when on a public forum.

(I currently cant comment as I used up all my rep for a bounty.)

Could you explain how you calculate the average? In you plot the averages are between an expression level of 2 and 3, while you report values over 10. Given the data you show, there is no significant difference and I would guess p-values are above 0.8!

And you mention that the violin plots suggest the control groups have higher expression.. but how do you see that? For me they are identical with minimal trends that the PLX5622 groups are higher.

And to address your question regarding showing the total: No, you would want to show the mean or median, as the total is pointless, given deviating sample sizes.

EDIT: Overall, I have a feeling you uploaded the wrong picture!

EDIT2: I think I got your point now: The difference in mean is caused by an increased number of outliers in your controls at the value 0. Despite those, the means are identical and this is what can be seen through the violin plots. You should rather try to diminish the effect of these outliers.