DESeq results gives all genes
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evocanres • 0
@evocanres-17914
Last seen 7 months ago
United States

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  |

design = ~ group)

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

[1] 35275


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

deseq2 design matrix results • 877 views
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Entering edit mode
@mikelove
Last seen 4 hours ago
United States

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

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Thank you. That helped actually.