What are less and greater in fc.kegg.p?

Question

[Parham]

Hi,

I am trying to do pathway analysis using this workflow. In section 6.1 part two I create a fc.kegg.p file. See it here. I wonder what are all the columns starting with greater/less? What is greater or less? I am new to this so my question may sound very stupid to you. But please let me know even if it is so basic! And in the end there are to columns stats.stat.mean and stats.exp1. What are them?

Thanks!

Answer 1

[Ming Tommy Tang]

I believe

less means the pathway is downregulated

greater means the pathway is upregulated.

[Parham]

I guess not, since a pathway cannot be both up and down-regulated! Besides in all the pathways you see with NA, among them I am sure some are down-regulated pathways that for some reason couldn't be calculated in this analysis!