Table 1 Analysis methods with their associated R packages and details concerning their implementation
Method | R-Package(s) | Multiple DF Test | Library Adjustment Offset | Details |
|---|---|---|---|---|
DESeq2 | DESeq2 [6] | LRT | DESeq2 size factors | Default settings used, correlation ignored. |
DESeq2 ∗ | DESeq2 [6] | LRT | DESeq2 size factors | Default settings used, subjects treated as fixed effects to account for correlation. |
edgeR | edgeR [4] | LRT | TMM offset | Default settings used, correlation ignored. |
edgeR ∗ | edgeR [4] | LRT | TMM offset | Default settings used, subjects treated as fixed effects to account for correlation. |
limma | Moderated F-test | NA | Count data transformed using the voom function. The duplicateCorrelation function was used with subject id as a blocking factor to account for correlation. | |
GEE | Custom R Functions, geepack [27] | Wald χ2 Test | DESeq2 size factors | Models fit using exchangeable working correlation structure. For small sample estimators, custom functions were created by modifying code from the geesmv package [28] to make it compatible with geepack and enable the use of offsets. |
LMM | lmerTest [29] | F-test | NA | Data transformed using the variance stabilizing transformation from the DESeq2 package. |
NBMM-AGQ | GLMMadaptive [30] | LRT | DESeq2 size factors | Model fit using the mixed_model function with a negative binomial distribution. Default settings used for all other parameters. |
NBMM-LP | glmmADMB [31] | LRT | DESeq2 size factors | Model fit using the glmmadmb function with a negative binomial distribution. Default settings used for all other parameters. |
NBMM-PL | Custom R Function | LRT | DESeq2 size factors | Custom function was created drawing from the glmm.nb function in the NBZIMM package [21]. Function was created to be compatible with the lmerTest package [29] in order for Satterthwaite degrees of freedom to be calculated. |
rmRNAseq | rmRNAseq [18] | Moderated F-statistic with bootstrapped p-values | NA | Model fit using the TC_CAR1 function with the default parameters. |