Question: DESeq results gives all genes
0
gravatar for evocanres
10 months ago by
evocanres0
evocanres0 wrote:

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 ?

deseq2 design matrix results • 221 views
ADD COMMENTlink modified 10 months ago by Michael Love25k • written 10 months ago by evocanres0
Answer: DESeq results gives all genes
2
gravatar for Michael Love
10 months ago by
Michael Love25k
United States
Michael Love25k wrote:

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

ADD COMMENTlink written 10 months ago by Michael Love25k

Thank you. That helped actually.

ADD REPLYlink written 10 months ago by evocanres0
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