Question: The number of the counts columns uploaded to the Deseq2 affected the number of reported DEG
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gravatar for naktang1
8 months ago by
naktang10
Thailand
naktang10 wrote:

I has just started using Deseq2 to discovery deferentially expressed genes (DEGs).

In my data, I have 6 strains (S2,S3,S4,S5,S6,S7), each of which was studied at 2 time points (T1,T2), under 2 conditions ( drought, water), and with 2 replicates.

I performed the analysis like this: 1) Upload counts data for all strains and all conditions (48 columns) to the deseq2 at once, performed comparison between "T1S2water" and "T1S2drought", and got 0 DEGs. 2) Upload counts data for T1S2water and T1S2drought (4 columns) to the deseq2, performed the same comparison, and got 4 DEGs. 3) Upload counts data for T1S2water, T1S2drought,T2S2water, and T2S2drought (8 columns), performed the comparison and got 23 DEGs.

I am wondered that Why the number of the columns uploaded to the Deseq2 affected the number of DEG. Note that the reported DEGs seem to involved in the drought response that I interested.

deseq2 • 202 views
ADD COMMENTlink written 8 months ago by naktang10
Answer: C: The number of the counts columns uploaded to the Deseq2 affected the number of r
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gravatar for Michael Love
8 months ago by
Michael Love25k
United States
Michael Love25k wrote:

This is a FAQ in the vignette.

ADD COMMENTlink written 8 months ago by Michael Love25k
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