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Question: DESeq results gives all genes
0
gravatar for evocanres
11 weeks 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 • 119 views
ADD COMMENTlink modified 11 weeks ago by Michael Love22k • written 11 weeks ago by evocanres0
Answer: DESeq results gives all genes
2
gravatar for Michael Love
11 weeks ago by
Michael Love22k
United States
Michael Love22k 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 11 weeks ago by Michael Love22k

Thank you. That helped actually.

ADD REPLYlink written 11 weeks ago by evocanres0
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