What type of statistics should I use to analyze output from metagenome classifier "Centrifuge"?
I have run Centrifuge on 24 samples from RNA-seq: 11 samples are a grade A of the disease, 11samples are grade B of the same disease and 2 samples are normal.
After that, I merged output into one file with rows as species and columns as samples. Next, I assumed it's better for me to use only numUniqueReads column, so I deleted the others columns from the merged file. After that, I supposed I can delete rows with only zero and NA results for all samples. Finally, I have a file with 25 columns and ~2000 rows.
I would be grateful if you could help me with this question.
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