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stefpeschel / NetCoMi

Network construction, analysis, and comparison for microbial compositional data
GNU General Public License v3.0
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Filtering before running Netcomi #100

Closed Anaskou closed 8 months ago

Anaskou commented 9 months ago

I am using Netcomi to create a network from meta transcriptomics using raw counts. Before running Netcomi I want to filter my taxa and keep only 100 of them. Can I give as input in netcomi the counts from only these taxa, or as the samples have different library sizes, this will create bias?

Thanks a lot !!!

stefpeschel commented 9 months ago

You can either use NetCoMi's internal functionality for taxa filtering (arguments filtTax and filtTaxPar), or you can filter the taxa in advance. The fact that samples have different library sizes, so that counts from different samples are not comparable, is a general problem independent of the filtering process. You're invited to read our manuscript to get familiar with the different normalization methods implemented in NetCoMi to account for different library sizes and also for compositionality.