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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Add soils reproducibility dataset to examples #58

Closed joey711 closed 12 years ago

joey711 commented 12 years ago

From their abstract: To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. . .

http://www.nature.com/ismej/journal/v5/n8/full/ismej201111a.html

I contacted the authors, and they provided me with some additional files that should be suitable for inclusion. If not, write back to them for additional data. Would be an interesting study to include

Would also be interesting to include an example for addressing the fraction of OTUs expected to be resampled between replicates.

joey711 commented 12 years ago

Included as of version 0.99.6. Still needs example code in the documentation, but this issue can be considered closed immediately.