How can I summarize Log2 Fold Change values for many genes within a treatment group?


I have 5 sets of Log2 Fold Change values pulled off DualSeqDB. Each of the 5 groups corresponds to a different microbial taxon. Within the 5 groups, there are many Log2 Fold Change values, each corresponding to a gene that was significantly affected by the presence of the microbe.

My question is: is there any way to get the average Log2 Fold Change for each group? How could I calculate that?

The end goal is to compare each microbe's effect on gene expression, hopefully to prove that the phenotype of the microbe is in some way related to how much it can change the gene expression in its host.

I have considered using p-values to compare each taxa's effect on gene expression, but because all the datasets are significant, the p-values I got using fisher's method are all 0, so I don't know how I could go ahead and compare that to categorical variables (like presence of a certain phenotype).

Thanks so much to anyone who can help!



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