RNAseq blood profiling of liver fibrosis during schistosomiasis

Metabolomics analysis was conducted by BGI China and the results were transferred by FTP. In addition to the raw and normalized quant data they also performed differential abundance testing, PCA, pathway enrichment etc. Justin Nono has requested that I redo these analyses and integrate with RNAseq profiles. See email correspondence below:
On a follow up note, I have just received the metabolomics results from BGI on the plasma samples (see attached and mail below). Please do not hesitate to retrieve the files , as instructed by the service provider and let us know how, at your convenience, what could be found from the bioinformatic analyses (comparative metabolite expression, untargeted)....I plan to have this done for RNA seq, Metabolomics and the upcoming metagenomics then see if an integration of the 3 platform results is possible to define robust combo of markers with high PPV or strong association with either infection and /or fibrosis.

The comparisons to be done are as follows, where no_merge, merge_D, merge_E refer to the folders made available for transfer from BGI

no_merge:
KK+US- 10 (group 2) vs. KK-US- (group 4)
KK+US+ 10 (group 1) vs. KK-US- (group 4)
KK+US+ 10 (group 1) vs. KK+US- (group 2)

merge_D:
KK+US- KK-US- 20 (group 2 + group 4)
vs.
KK+US+ KK-US+ 20 (group 1 + group 3)

merge_E: metabolites that might regulate infection overall
KK-US- 10 (group 4)
vs.
KK+US+ KK+US- 20 (group 1 + group 2)