Table 1 Methods and parameter configurations compared in this paper
Key | Software | Configuration parameters |
|---|---|---|
DESeqPgO | DESEq | method=~pooled~, sharingMode=~per-condition~ |
DESeqPmax | DESEq | method=~pooled~, sharingMode=~maximum~ |
DESeqCgO | DESEq | method=~per-condition~, sharingMode=~per-condition~ |
DESeqCmax | DESEq | method=~per-condition~, sharingMode=~maximum~ |
edgeRdf20 | edgeR | common/trended/tagwise moderation regime with prior.df=20 (default) |
edgeRdf1 | edgeR | common/trended/tagwise moderation regime with prior.df=1 |
edgeRqlfDf20 | edgeR | common/trended/tagwise moderation regime with prior.df=20 (default) and quasi-likelihood F-tests |
edgeRqlfDf1 | edgeR | common/trended/tagwise moderation regime with prior.df=1 and quasi-likelihood F-tests |