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Linear Decomposition Model
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LDM package analyses data processed by other normalisation methods (e.g. CSS) #5

Open JialinHe0o0 opened 1 year ago

JialinHe0o0 commented 1 year ago

Dear yijuanhu, I would like to use the LDM package to analyze data processed by other normalization methods (e.g. CSS), do I need to add the following parameters in the ldm() function, such as: scale.otu.table = F, center.otu.table = F Thanks!

yijuanhu commented 1 year ago

Hi, You should set scale.otu.table=F if you have applied CSS normalization. You should still use center.otu.table=T to help with model fitting. In addition, you should set freq.scale.only=T to suppress the arcsin-root transformation of data since your data have been normalized.

Yijuan

JialinHe0o0 commented 1 year ago

Thank you so much for your answer! I have been troubled by such questions for several days and your answers were very helpful to me.

With gratitude, HJL0912

yijuanhu commented 1 year ago

Sorry that I missed your email for many days.

Yijuan

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On Mar 9, 2023, at 4:19 AM, HJL0912 @.***> wrote:



Thank you so much for your answer! I have been troubled by such questions for several days and your answers were very helpful to me.

With gratitude, HJL0912

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