sw1
commented
5 years ago As long as you make your data matrices look the same as the input in the david tutorial you should be fine. Have you tried that? Any trouble? str() and the like are your friends here.
Sorry for the delayed response btw.
Steve
From: owenNewcastle notifications@github.com Sent: Thursday, February 28, 2019 8:53 PM To: EESI/themetagenomics Cc: Subscribed Subject: [EESI/themetagenomics] Output file from dada2 to use in Tax4Fun (#5)
I'm investigating biofilms living on plastic debris. I want to find out if there is differential expression of certain KEGG Orthologs (KO) at week 0 and week 7 of my microcosm experiment (as well as between different treatments - all of which are variables in my phyloseq object.
I am trying to work from this tutorial: https://cran.r-project.org/web/packages/themetagenomics/vignettes/thematic_structure.html (see sections titled Preprocessing and Functions)
How would I convert my dada2 output (or phyloseq object) into a format similar to the DAVID dataset mentioned in this tutorial??
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ivanepg
I'm investigating biofilms living on plastic debris. I want to find out if there is differential expression of certain KEGG Orthologs (KO) at week 0 and week 7 of my microcosm experiment (as well as between different treatments - all of which are variables in my phyloseq object.
I am trying to work from this tutorial: https://cran.r-project.org/web/packages/themetagenomics/vignettes/thematic_structure.html (see sections titled Preprocessing and Functions)
How would I convert my dada2 output (or phyloseq object) into a format similar to the DAVID dataset mentioned in this tutorial??