yeast-insilico: Yeast in silico dataset results

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

Yeast in silico dataset results

Description

Results for differential gene expression analysis using in silico (computationally) spiked-in data generated 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:

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

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

• yeastH-results-de5: using unimodal alternative, 500 DE genes, strong informative covariate, 5 vs. 5 comparison.

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

• yeastIIH-results-de5: using bimodal alternative, 500 DE genes, strong informative covariate, 5 vs. 5 comparison.

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

• yeastHW-results-de5: using unimodal alternative, 500 DE genes, weak informative covariate, 5 vs. 5 comparison.

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

• yeastIIHW-results-de5: using bimodal alternative, 500 DE genes, weak informative covariate, 5 vs. 5 comparison.

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

• yeastH-results-de5-uninfCov: using unimodal alternative, 500 DE genes, uninformative covariate, 5 vs. 5 comparison.

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

• yeastIIH-results-de5-uninfCov: using bimodal alternative, 500 DE genes, uninformative covariate, 5 vs. 5 comparison.

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

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

• yeastH-results-de10: using unimodal alternative, 500 DE genes, strong informative covariate, 10 vs. 10 comparison.

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

• yeastIIH-results-de10: using bimodal alternative, 500 DE genes, strong informative covariate, 10 vs. 10 comparison.

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

• yeastHW-results-de10: using unimodal alternative, 500 DE genes, weak informative covariate, 10 vs. 10 comparison.

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

• yeastIIHW-results-de10: using bimodal alternative, 500 DE genes, weak informative covariate, 10 vs. 10 comparison.

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

• yeastH-results-de10-uninfCov: using unimodal alternative, 500 DE genes, uninformative covariate, 10 vs. 10 comparison.

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

• yeastIIH-results-de10-uninfCov: using bimodal alternative, 500 DE genes, uninformative 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

polyester-insilico

Examples

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

## Not run: 
`yeast-results-de5`()
`yeast-results-de5-uninfCov`()
`yeast-results-de10`()
`yeast-results-de10-uninfCov`()
`yeast-results-null5`()
`yeast-results-null10`()
`yeastH-results-de5`()
`yeastH-results-de5-uninfCov`()
`yeastH-results-de10`()
`yeastH-results-de10-uninfCov`()
`yeastHW-results-de5`()
`yeastHW-results-de10`()
`yeastII-results-de5`()
`yeastII-results-de5-uninfCov`()
`yeastII-results-de10`()
`yeastII-results-de10-uninfCov`()
`yeastIIH-results-de5`()
`yeastIIH-results-de5-uninfCov`()
`yeastIIH-results-de10`()
`yeastIIH-results-de10-uninfCov`()
`yeastIIHW-results-de5`()
`yeastIIHW-results-de10`()
`yeastIIW-results-de5`()
`yeastIIW-results-de10`()
`yeastW-results-de5`()
`yeastW-results-de10`()

## End(Not run)

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