Data without time series factor

[Bora Kim]

Hello, I would like to thank you for the package eLSA. It is very nice package to analyse time series work.

Unfortunately, my current microbiome data set doesn't have any time series factors. Instead, it has 3 replicates of 16 genotypes.

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1. I am wondering if I can consider this factors (without time series, genotypes) in command line.

I have tried this : root@fcec0005790b:/var/data# lsa_compute foroot.txt foroot.lsa -r 3 -s 16 -d 1

But I assumed, I should not include any parameters (such as -r, -s, -d)

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2. According to your paper published in 2011, BMC, I see that F-transformation is done before calculation. Does it mean that raw data is recommended to use?

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3. Finally, I am curious that if I can analyze both bacterial OTUs and fungal OTUs in one table. So far I used to normalize each OTUs separately and then pull in one table for the analysis.

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I would very much appreciate if I can have any advice from you.

Have a good day.

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[ohnoplus]

Are your data a time-series at all? Other tools may be better if not. That said, if you have some reason to use this anyway, you can set -`d 0`. You should still normalize your data to relative abundance before running it though elsa. You can include both bacterial and fungal OTUs together, just list as seperate columns. When I did something similar, I normalized them separately.