This module allows to perform the normalization and the differential expression analysis on expression step results. This module is based on the DESeq2 package of Bioconductor.
Parameter | Type | Description | Default value |
---|---|---|---|
norm.fig | boolean | If true, generate the figures of the normalization. | true |
diffana.fig | boolean | If true, generate the figures of the differential analysis. | true |
norm.diffana | boolean | If set to false, skip the normalization and the differential analysis. This option is used to produce the contrast matrix without doing the normalization and the differential analysis. | true |
diffana | boolean | If set to false, skip the differential analysis. | true |
size.factors.type | string | Determination of the size factors type to use during the differential analysis (value: ratio or iterate). | ratio |
fit.type | string | Determination of the fit type for the distance estimation to use during the differential analysis (value: parametric, local or mean). | parametric |
statistical.test | string | Statistical test to be used during the differential analysis (value: Wald or LRT). | Wald |
r.execution.mode | string | The R execution mode. The available mode values are: process, rserve and docker. | process |
rserve.servername | string | The Rserve server name to use in rserve execution mode | not set |
docker.image | string | The Docker image to use in Docker execution mode. | bioconductor/release_sequencing:3.1 |
Eoulsan differential expression analysis module use R with the package DESeq2 as statistical backend and FactoMineR. Differential analysis module was tested with R 3.2.0, DESeq2 1.8.1 and FactoMineR 1.28. You can install DESeq2 and FactoMineR R packages on your computer or on a Rserve server, or you can use the docker containing all the packages needed to run deseq2: bioconductor/release_sequencing:3.1 docker image. These packages are also present on the Eoulsan docker: Eoulsan docker.
DESeq2 can be used in 2 different modes: classic mode or contrast mode.
The classic mode performs the differential analysis on the "Condition" column of the design file. During the differential expression analysis each condition is compared to the others. The "Reference" column can be used to specify references for the comparison.
Exp.1.name=exp1 Exp.1.skip=false Exp.1.reference=WT-day1
The keys "reference" is optional and can be replaced by a "Reference" column in the design file.
The contrast mode performs the differential analysis using contrast vector.
Exp.2.name=exp2 Exp.2.skip=false Exp.2.contrast=true Exp.2.buildContrast=true Exp.2.model=~type+day+type:day Exp.2.comparisons=WT1_vs_KO1:typeWT%dayday1_vs_typeKO%dayday1;\ WT2_vs_KO2:typeWT%dayday2_vs_typeKO%dayday2