Correcting Farm effects

Question

[Jeyamalar]

Dear all,

My experiment was performed in 2 different farms and I have 16S rRNA sequences from these 2 farms. When I analysed the data, I observed strong farm effects. How to correct the farm effects to identify the true treatment effect? Is it Ok to correct for the farm effect or need to analyse these 2 farms separately? I tried the combat function and got negative values in the feature table. I do not think this is Ok. Can anyone help me on this?

Thank you

[Chris Dean]

It would be helpful to include additional information about your study design and a description of the primary objectives of your study. As you probably know, farms can have very different environments and management practices and this can have a major impact on the microbiome. Therefore, it seems plausible that the effect of your independent variable may vary between farms. Given this, I would recommend testing for an interaction between your independent variable and farm, and then stratifying your analysis by farm in the presence of a statistically significant interaction.

[ATpoint]

Add farm as a covariate into your differential abundance model to correct for it.