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yiluheihei / microbiomeMarker

R package for microbiome biomarker discovery
https://yiluheihei.github.io/microbiomeMarker
GNU General Public License v3.0
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contrast for multiple groups (edgeR) #70

Closed ignadb closed 2 years ago

ignadb commented 2 years ago

Hi Yang,

Thanks so much for developing microbiome marker. It is very useful!

Now I am using it to analyse my data, which has 4 groups. I would like to use edgeR for the analysis. I however got some questions concerning contrast. In the manual of microbiome marker (under details toward the end of page 45), it says .. "users do required to concern this parameter (set as default NULL), and if there are two groups, the first level of groups will set as the reference group; if there are multiple groups, it will perform an ANOVA-like testing to find markers which difference in any of the groups".

In my case, I have multiple groups and I would like to perform an ANOVA-like testing. Shall I leave it as default (NULL)? Or should I set it something else? Thanks a lot and looking forward to hearing from you.

Best regards, Chatchai

yiluheihei commented 2 years ago

Hi @ignadb Thanks for your interested in microbiomeMaker. To perform an ANOVA-like tesing, you can leave contrast as the default NULL