Thank you for the help forum. I am first time working on Metagenomics. I have a clarification on the downstream processing step.
I downloaded the IBDMDB
processed functioan profile 3.0 from (https://ibdmdb.org/tunnel/public/HMP2/WGS/1818/products). The downloaded files have gene_families with CPM normalization.
The next step is to perform differential analysis. I am trying to compare the results between aldex2 and simple wilcoxon test.
For simple wilcoxon test, Can I provide the CPM normalized counts directly as input or should i convert it into relative abundance?
and for Aldex2, it requirs raw counts as it perform internal clr transformation. Can i simply roundup the CPM counts and give as input?
If the above method is not appropriate, kindly suggest the suitable method
And is it possible to get the relative abundance of functional profiles for IBD dataset?
Thank you in advance