Hi, I would appreciate any suggestions. I have three genotypes and two treatments.

kable(readCountColData)
sampleList |genotype |timePoint |group  |
|:----------|:--------|:---------|:------|
|WT_0_1     |WT       |0         |WT_0   |
|WT_0_2     |WT       |0         |WT_0   |
|WT_0_3     |WT       |0         |WT_0   |
|KO1_0_1    |KO1      |0         |KO1_0  |
|KO1_0_2    |KO1      |0         |KO1_0  |
|KO1_0_3    |KO1      |0         |KO1_0  |
|OV_0_1     |OV       |0         |OV_0   |
|OV_0_2     |OV       |0         |OV_0   |
|OV_0_3     |OV       |0         |OV_0   |
|WT_12_1    |WT       |12        |WT_12  |
|WT_12_2    |WT       |12        |WT_12  |
|WT_12_3    |WT       |12        |WT_12  |
|KO1_12_1   |KO1      |12        |KO1_12 |
|KO1_12_2   |KO1      |12        |KO1_12 |
|KO1_12_3   |KO1      |12        |KO1_12 |
|OV_12_1    |OV       |12        |OV_12  |
|OV_12_2    |OV       |12        |OV_12  |
|OV_12_3    |OV       |12        |OV_12  |


ddsReadCount <- DESeqDataSetFromMatrix(countData = readCount,
                                     colData = readCountColData,
                                     design = ~ group)
ddsReadCountSE <- DESeq(ddsReadCount)

resIVb <- results(ddsReadCountSE, contrast = c("group", "WT_0", "KO1_0"),
                 alpha = 0.05)                                     
nrows(resIVb)
[1] 35275

nrow(readCount_raw)
[1] 35275

Why I am getting the same number of genes after performing differential analysis ?

Take a look at the vignette or the workflow, which will help in how to understand and work with the results table.