RNA-seq results comparison possible or not?

Question

[mahnazkiani]

I have 2 sets of data for my plant, the first set included 3 biological reps from plants that grown in 3 different times and got the samples from 2 parts of the stem to compare cell wall genes expression, my second set of plants grown in different light condition but still have 2 biological reps. Now I want to see does light affect the cell wall gene expression or not? Can I do this comparison between these 2 sets of data? How about the batch effects? The problem is that I didn't include any control in second sets of plants and I don't know how I can find about the batch effects or is it even possible to adjust the batch effects?

Thanks

[Benn]

If your 2 experiments are performed in 2 separate batches, it doesn't make sense to include the batch in your model.