Example replication

[theo-allnutt-bioinformatics]

Hi, I am trying to replicate your example with my own data. The methods for getting the data into the model are extremely complicated, to the point of not being repeatable with any other data set. Do you have any plans to make this process simpler, e.g. input biom file with metadata from QIIME or metaphlan? If not, then I fear that your methodw ill not be used by other researchers. Thanks.

T.

[chvlyl]

Thanks for your interest in ZIBR. The input to ZIBR is simply a table (please refer to the ibd.data in the README example). I also provided some R code to transform the data into the format that ZIBR can take. I don't think it is very difficult to write some code to transform your own data into such a table. From the feedback I received, many researchers already used ZIBR on their own dataset.

If you can provide more details about the specific difficulty you have, rather than just the strong statement, I am happy to help you.

[theo-allnutt-bioinformatics]

I think the problem is in the "Real data (reproduce the analysis in my Bioinformatics paper)" example - in trying to replicate trying to load actual data. The example is very specific to your actual data. Is it possible to provide two examples, e.g. one loading data where metadata (in metagenomics parlance, i.e. cofactors) is in the same table as the abundances, and perhaps another where the metadata is separate (OTU tables often being in different orientation to metadata, or 'mapping' files, from e.g. QIIME). There are a lot of transformations and conversions in your example that are not clear why they are being made. I presume this is to get the cofactor data into the correct format, but we don't know what that is from your annotation. Thanks for your help. T.