Chuck Pepe-Ranney edited Results.tex  almost 10 years ago

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In bacterial libraries, sequences were distributed into 636 total OTUs; 58\% of quality controlled sequences fell into the top 25 OTUs in order of decreasing sum of relative abundance across all samples. 23S plastid rRNA gene sequences were distributed into 359 total OTUs; 71\% of sequences fell into the top 25 OTUs sorted by mean relative abundance across all samples. Rank abundance curves for each mesocosm specific pair of planktonic and biofilm samples showed planktonic communities to be more sharply skewed in both the algal and bacterial datasets (Figure 9).   We used the RNA-Seq differential expression statistical framework developed by \citet{deseq} (for review of RNA-Seq differential expression statistics applied to microbiome OTU count data see \cite{24699258}). We use the term "differential abundance" (coined by \citet{24699258}) to denote OTUs that have different mean proportions across sample classes. We are particularly interested in two sample classes: 1) environment type (biofilm or planktonic) and, 2) high carbon (C:P = 500) versus not high carbon (C:P = 10, C:P = 100 and C:P = control). A differentially abundant OTU, for instance, would have a mean proportion in one class that is statistically different from its mean in another. This differential abundance could mark an enrichment in either class and the direction of the enrichment is apparent in the sign (positive or negative) of the metric used summarize the mean proportion difference. Here we use log$_{2}$ of the mean proportion ratio (means are derived from OTU proportions for all samples in each given class) as our differential abundance metric. It is also important to note that the DESeq2 R package we're we are  using to calculate the differential abundance metric "shrinks" the metric in inverse proportion to the information content for each OTU. In this way the differential abundance metric will be high only for OTUs for which we have strong confidence of true differential abundance and the metric can be used to effectively rank OTUs by magnitude of the sample class affect. The DESeq2 RNA-Seq statistical framework has be shown to improve power and specificity when identifying differentially abundant OTUs across sample classes in microbiome experiments \cite{24699258}. To probe how