Empirical analysis of DGE - implementation parameters
The 'Empirical analysis of DGE' algorithm in the CLC Genomics Workbench is a re-implementation of the "Exact Test", available as part of the EdgeR Bioconductor package.
The parameter values used in the CLC Genomics Workbench implementation are the default values for the equivalent parameters in the EdgeR Bioconductor implementation in all but one case. The exception is the estimateCommonDisp parameter.
The parameter values used in the CLC Genomics Workbench implementation, with reference to the EdgeR function names for clarity, are provided in the table below.
| Function in BioC package | Parameter name | Value used and comments |
| calcNormFactors | method | "TMM" |
| refColumn | NULL (automatically selected) | |
| logratioTrim | 0.3 | |
| sumTrim | 0.05 | |
| doWeighting | TRUE | |
| Acutoff | -1e10 | |
| estimateCommonDisp | tol | 1e-14 (default in edgeR: 1e-6) |
| rowsum.filter | Set by user in wizard ("Total count filter cutoff", default 5) | |
| estimateTagewiseDisp | prior.df | 10 |
| trend | "movingave" | |
| span | NULL | |
| method | "grid" | |
| grid.length | 11 | |
| grid.range | c(-6, 6) | |
| mglmOneGroup | maxit | 50 |
| tol | 1e-10 | |
| aveLogCPM | prior.count | 2 |
| dispersion | 0.05 | |
| exactTest | pair | Set by user in wizard ("Exact test comparisons") |
| dispersion | "auto" (tagwise if available, otherwise common) | |
| rejection.region | "doubletail" | |
| big.count | 900 | |
| prior.count | 0.125 |