MetagenomeSeq: analysing paired samples
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@marypadilha-11999
Last seen 4.7 years ago

Hi,

I am working with microbiome samples before and after a diet intervention, and using the fitZig function for the statistics analysis. However, I would like to compare them as paired samples. Is there a specific function for paired sample analysis?

Thank you for your attention,

Best regards,

Marina

metagenomeseq paired samples microbiome • 624 views
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jananee15 • 0
@jananee15-23229
Last seen 16 months ago

Hi, I see you are in a similar situation as mine. I used "duplicate correlation" from the limma package and that allows you to add the study subject (I suppose) as repeat variable. You can use the output of duplicate correlation (which is a list), in the fitzig while using the "usemixedmodel = dup$corr". Also please beware while choosing your features, remember to use the "calculate effective size" as suggested by the authors. Good luck!

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