Question: How to perform DEseq2 on datasets without replicates or merged replicates
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gravatar for aishu.jp
11 days ago by
aishu.jp20
aishu.jp20 wrote:

I have a plant RNA seq data of control and treated conditions obtained from 4 different days. This SRA dataset obtained from NCBI doesn't have replicates but have mentioned in their article that they have merged the biological replicates drawn during sequencing process in the sample preparation section. When I try to run DESeq, I am getting error because of the absence of replicate sample read counts. How can obtain the differential expressed genes between control and treated of each day separately?

Can anyone please help me how to solve this.

ADD COMMENTlink modified 10 days ago by swbarnes2340 • written 11 days ago by aishu.jp20
Answer: How to perform DEseq2 on datasets without replicates or merged replicates
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gravatar for Michael Love
10 days ago by
Michael Love26k
United States
Michael Love26k wrote:

DESeq2 requires replicates to perform statistical inference. It cannot do a 1 vs 1 comparison.

ADD COMMENTlink written 10 days ago by Michael Love26k
Answer: How to perform DEseq2 on datasets without replicates or merged replicates
0
gravatar for swbarnes2
10 days ago by
swbarnes2340
swbarnes2340 wrote:

With just one sample of each kind, there is no use for fancy statistics. You can use the library normalization techniques described in DESeq, and then just compare the values directly. You won't be able to generate a p-value.

ADD COMMENTlink written 10 days ago by swbarnes2340
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