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Thread: Performing a Simple Network Analysis

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    Performing Network Analysis on OTU data




    Hi,

    I have recently been trying to carry out network analysis to study the community structure of bacteria (OTUs) within the gut of mice. I have 102 samples from 15 mice, each sample corresponding to a certain section along the gastrointestinal tract. I have so far used the package 'phyloseq' in R to organise the data to show me the number of detected sequences in each sample at the family level. I would like to study the intra and inter differences in bacterial communities and composition within and between individuals.

    I am using igraph to view the networks, but at the moment i am relatively new to R software and to network analysis. I have so far tried to perform analyses by studying the co-occurrence patterns, but without much success. My main concern at the moment for co-occurrence is the pre-processing of data before creating a network. Most papers use some form of significance test before applying a False Discovery Rate correction to the resultant p-values, but as i said i'm pretty ignorant in this area and don't know where to start with these steps. Any help with pre-processing of data and network analysis would be greatly appreciated, and i am open to any alternative methods. Feel free to ask for any additional information. Thankyou

    Kez
    Last edited by KezOmalley; 07-04-2014 at 04:02 AM.

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