Question: DESeq results gives all genes
0
gravatar for evocanres
12 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 • 246 views
ADD COMMENTlink modified 12 months ago by Michael Love26k • written 12 months ago by evocanres0
Answer: DESeq results gives all genes
2
gravatar for Michael Love
12 months ago by
Michael Love26k
United States
Michael Love26k 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 12 months ago by Michael Love26k

Thank you. That helped actually.

ADD REPLYlink written 12 months ago by evocanres0
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