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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.
metadata |
logical whether to load metadata (TRUE) or full resource (FALSE). (default = FALSE) |
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.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | `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)
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