Before I get into CLR transformation, is there any step to change my OTU table ?

General Discussion
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Hello ! Folks.

I'm trying integrate OTU table data from different batches.

Hence, I'm considering to do normalization before any further analysis.

I have looked through normalization methods and found that Centered Log ratio was one of the most mentioned method.
(I know it is built in many plug in of qiime. But I have to do other analysis in addition to the functions in qiime2)

However, I found that a sentence saying "Make Pseudocount before CLR"). Is there any pre-step before do CLR transformation ? Or the pseudocount would be made in the normal process integrated in CLR transformation ? I will use R, ALDEx2 package / or Python sckit-bio package to do my table transformation to CLR form.

Please suggest me and explain me about the question.

Many thanks for your help.

2

Hello!
To get CLR data like in aldex2, I used this code:

import pandas as pd
from skbio.stats.composition import clr


# Function from absolute abundances to clr
def to_clr(data):
    data += 1                                  # add pseudocount
    data = data.div(data.sum(axis=0), axis=1)  # relative abund
    return pd.DataFrame(clr(data.T), columns=data.index, index=data.columns).T #clr

As well as I remember I got identical results as in aldex2.
So, I added pseudocounts, converted to relative abundances and applied CLR from skbio. It was also neccessary to transpose the data before clr and then transpose it back.

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Thank you tomanix !! This would be a definitely big help for me ^^ I'll try this and match the result from R.

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