Differential Expression Comparisons

[ronaldrcutler]

Hello all. In a DE experiment concerning a gene of interest there is an upregulated condition, downregulated condition and control. When comparing these using DESeq, it obviously makes sense to compare both conditions against the control. However, when comparing the upregulated condition against the downregulated condition, what are we getting out of this and how can we interpret this?

[dpryan]

You're getting whatever the difference between then is (either very upregulated or very down regulated, depending on which way the comparison is made).

[mhkiani]

RNA-seq results comparison possible or not?

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?