Experiment details: Genotypes: DJ and IR (Ref: IR) Tissues: L1, L3 and R (Ref: R) Treatments: HP.S, LP.C, LP.S and HP.C (Ref: HP.C)
design = ~Genotypes * Tissues * Treatments
resultsNames(dds)
GenotypesDJvsIR
GenotypesDJ.TissuesL1
GenotypesDJ.TissuesL1.TreatmentsHP.S GenotypesDJ.TissuesL1.TreatmentsLP.C GenotypesDJ.TissuesL1.TreatmentsLP.S GenotypesDJ.TissuesL3 GenotypesDJ.TissuesL3.TreatmentsHP.S GenotypesDJ.TissuesL3.TreatmentsLP.C GenotypesDJ.TissuesL3.TreatmentsLP.S GenotypesDJ.TreatmentsHP.S
GenotypesDJ.TreatmentsLP.C GenotypesDJ.TreatmentsLP.S
Intercept TissuesL1vsR TissuesL3vsR
TissuesL1.TreatmentsHP.S TissuesL1.TreatmentsLP.C TissuesL1.TreatmentsLP.S TissuesL3.TreatmentsHP.S
TissuesL3.TreatmentsLP.C
TissuesL3.TreatmentsLP.S
TreatmentsHP.SvsHP.C TreatmentsLP.CvsHP.C"
TreatmentsLP.SvsHP.C
Could someone please have a quick look at my following 'contrasts'? Are my sub-headings correct for the corresponding contrasts?
HP.S effect (across all tissues) on IR:
HPS_IR <- results(dds, contrast = c("Treatments","HP.S","HP.C"), alpha = 0.005)
HP.S effect (across all tissues) on DJ:
HPS_DJ <- results(dds, contrast = list(c("Treatments_HP.S_vs_HP.C","GenotypesDJ.TreatmentsHP.S")), alpha = 0.005)
LP.C effect (across all tissues) on IR:
LPC_IR <- results(dds, contrast = c("Treatments","LP.C","HP.C"), alpha = 0.005)
LP.C effect (across all tissues) on DJ:
LPC_DJ <- results(dds, contrast = list(c("Treatments_LP.C_vs_HP.C","GenotypesDJ.TreatmentsLP.C")), alpha = 0.005)
LP.S effect (across all tissues) on IR:
LPS_IR <- results(dds, contrast = c("Treatments","LP.S","HP.C"), alpha = 0.005)
LP.S effect (across all tissues) on DJ:
LPS_DJ <- results(dds, contrast = list(c("Treatments_LP.S_vs_HP.C","GenotypesDJ.TreatmentsLP.S")), alpha = 0.005)
HP.S effect on genotype IR tissue L1:
HPS_IR_L1 <- results(dds, contrast = list(c("Treatments_HP.S_vs_HP.C", "TissuesL1.TreatmentsHP.S")), alpha = 0.005)
HP.S effect on genotype DJ tissue L1:
HPS_DJ_L1 <- results(dds, contrast = list(c("TissuesL1.TreatmentsHP.S", "GenotypesDJ.TissuesL1.TreatmentsHP.S")), alpha = 0.005)
Thank you very much.
