Question: DEseq2 analysis time-series data under two conditions
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gravatar for Cindy
5 days ago by
Cindy0
Cindy0 wrote:

I have time series data from two condition, like 0h, 2h, and 6h by treatment A and B. I want to know FDR different between A and B at 1h fold change for example compared with their individual 0h. in other word, I want to subtract 0h expression first and then compare the two 1h secondly (take 1h for example). And I want to know every time point different compared with 0h between two treatments. I already have all count files for each time point and each treatment. How I can design in DEseq2? Could I have an example code for this?

deseq2 • 67 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by Cindy0

Thank you so much. I am reading the workflow now. And I am trying to apply my count data in it, but now I can not even get the count data into DESeq2. My count matrix is txt file and each row represents an gene, each column represents a sample.

ADD REPLYlink written 5 days ago by Cindy0

If the workflow and vignette are not sufficient you may want to collaborate with a bioinformatics group. It’s beyond the scope of the support site.

ADD REPLYlink written 5 days ago by Michael Love24k

Yes, thank you. I am not computer people, looks I need help from bioinformatics group. Thank you again.

ADD REPLYlink written 5 days ago by Cindy0
Answer: DEseq2 analysis time-series data under two conditions
0
gravatar for Michael Love
5 days ago by
Michael Love24k
United States
Michael Love24k wrote:

Please first take a look at the time series example in the DESeq2 workflow.

ADD COMMENTlink written 5 days ago by Michael Love24k
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