What kind of ANOVA is suitable for this kind of experimental Design

[august]

Hello All,

I'm working with some metabolic data, which has the following design:
Cells were grown under two Nutrient conditions separately (Nt1 & Nt2) and for four types of cells each expressing Only any of the three subtype of a particular enzyme (sub1, sub2 or sub3) the fourth cell type has all the sub types of that enzyme knocked out (KO).

So there are four cell types under two nutrient conditions and for each cell /condition combinations I've four biological replicates.

Here's an abridged example of data:

Anova.png

The complete data for the two metabolites are avaiable in Pastebin


What kind of ANOVA is suitable for this study and can somebody please provide any R code snippet to do that?

Thanks