I have 7 individuals split into two groups (W=3, R=4). For each individual, I classified their transcriptome reads using Kraken against the Silva database, and now have a list of the number of reads classified for each of the ~851 genera matched within the database (example attached). We want to see if there is a significant difference in the number of reads for each species between the treatment and control groups.
So far:
- T-test by matched species has 9 species that have 0.006
If the your data are transposed into a Between x Within Design as in the 'Transposed' sheet of the Kraken_sample Excel data in attachment, you could run non-parametric tests. If the design is correct, there is a sign. effect of Transcripts, Group and the interaction, with the ARTool (http://depts.washington.edu/acelab/proj/art/index.html ) and the nparLD non-parametric tests.
Jos Feys You have done what I thought was impossible: sending an R script that works flawlessly on another user's desktop! Thank you very much for your time in putting this together and thorough response - this will help us a lot in our project moving forward. I hadn't heard of the ARTool or the nparLD np tests, so these are a good direction to move in.
Thank you again!
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