Different read numbers for the same samples

Question

[Luke]

I have 5 groups of interest for my rnaseq, where I also broke it down into a 3 group version for simplicity. What I am confused by is when I look at the single gene reads for the same groups in different analysis scripts, I get different read values. Can someone spot my error or explain what is happening? figures below.

[Ram]

Why did you delete the post?

Answer 1

[swbarnes2]

This pictures don't help, posing images of your code is not so great either. If you must post so much of it, post it as text, formatted to be code.

Forget the pictures. Show us what you get when you query the dds object for the values for that gene.

At a glance, it's not entirely clear to me that the left and right halves are doing the same thing, since the coldata$names could be different.