I´m using the metagenomSeq package to normalize my 16S data for one experiment with several samples . Here below are the log2 boxplots of the data after normalization ( i have normalized at the genus level). It looks that the normalization has worked pretty well. I have tried to check the data with qqnorm (2nd graph below).In the qqnorm graph the data does not look very normal ???? I still see a lot of values close to (>0) , i assume these are basically singletons.
I´m just wondering if this is what you expect from such metagenomics data and if i can apply normality tests (such as anova for eaxmple) to compare my groups or i should stick to the suggested methods in metagenomeSEQ for gorup comparisons. How can i control my data has properly been normalized. Thanks for your advice.