I am working on RNAseq data analysis using DESeq2 R package.
I havemy code
dds <- DESeqDataSetFromMatrix(countData = count.mat , colData = cond, design = ~Strain + Time) to create the matrix.
My confusion is with the design formula
design = ~Strain + Time where I have
Time variables to compare in my colData for my countData matrix.
This is my
count1 1 1
count2 1 1
count4 1 2
count5 1 2
count13 2 1
count14 2 1
count16 2 2
count17 2 2
countX 2 3
I want to understand the difference between these four designs that could go in the function
a) `design = ~Strain + Time + Strain:Time`
b) `design = ~Strain + Time`
c) `design = ~Time`
and d) `design = ~Strain`
My understanding is that the DESeq2 takes the last variable in the design formula (here Time) as a control variable, so to test for different samples in Time group, I have these codes below. So, I want to know what the outputs of
resultNames(ddsTC) really mean?
ddsTC <- DESeqDataSet(dds, ~ Strain + Time ) ##For time
ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~Time ) #For Time
 "Intercept.1" "Time_3_vs_1.1" "Time_2_vs_1.1" "Strain_2_vs_1.1"