Comparing whole transcriptome under one condition to the transcriptomes under other conditions

Question

[Texx]

I have 3 different conditions with quite a few samples (of RNAseq data) of how a certain bacterial organism behaves under these conditions. Now I'd like to add another condition and sequence the transcriptome of this same bacterial species.

What I'd like to know is to which of the previous three conditions is the transcriptome of my bacterium most similar under this new condition. What would be some (established) methods that are used in such cases? What metrics could be used to evaluate the differences and similarities?

Thank you in advance!

[dthorbur]

So you're adding a new condition to an already finished experiment?

Firstly, you would likely need to re-sequence a new control just in case your stocks have changed slightly (or other possible effects) in the time between the first experiment and now.

You can use almost any ordination analysis (e.g., PCA, PCoA, NMDA) and something like an ANOSIM would be a reasonable fit here. Packages like vegan in R are useful.