polyester-insilico: Polyester simulated dataset results

In stephaniehicks/benchmarkfdrData2019: Data and Benchmarking Results from Korthauer and Kimes et al. (2019)

Polyester simulated dataset results

Description

Results for differential gene expression analysis using RNA-seq data simulated with the Polyester package from yeast data obtained from Schurch et al. (2016) as described in Korthauer and Kimes et al. (2019). Differential expression was tested using DESeq2.

Arguments

metadata

logical whether to load metadata (TRUE) or full resource (FALSE). (default = FALSE)

Details

Results for this case study include:

• polyester-results-null5: null 5 vs. 5 comparison.

• polyester-results-de5: using unimodal alternative, 2000 DE genes, strong informative covariate, 5 vs. 5 comparison.

• polyester-results-de5-uninfCov: using unimodal alternative, 2000 DE genes, uninformative covariate, 5 vs. 5 comparison.

• polyesterW-results-de5: using unimodal alternative, 2000 DE genes, weak informative covariate, 5 vs. 5 comparison.

• polyester-results-null10: null 10 vs. 10 comparison.

• polyester-results-de10: using unimodal alternative, 2000 DE genes, strong informative covariate, 10 vs. 10 comparison.

• polyester-results-de10-uninfCov: using unimodal alternative, 2000 DE genes, uninformative covariate, 10 vs. 10 comparison.

• polyesterW-results-de10: using unimodal alternative, 2000 DE genes, weak informative covariate, 10 vs. 10 comparison.

References

• Schurch, N. J. et al. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?. RNA, 22(6), 839-851.

See Also

yeast-insilico

Examples

`polyester-results-de5`(metadata = TRUE)

## Not run: 
`polyester-results-de5`()
`polyester-results-de5-uninfCov`()
`polyester-results-de10`()
`polyester-results-de10-uninfCov`()
`polyester-results-null5`()
`polyester-results-null10`()
`polyesterW-results-de5`()
`polyesterW-results-de10`()

## End(Not run)

stephaniehicks/benchmarkfdrData2019 documentation built on April 13, 2025, 9:02 p.m.