Question: Comparison of samples of different time points using DESeq2.
0
gravatar for snu_jh
6 weeks ago by
snu_jh0
snu_jh0 wrote:

Hello,

I have a question about analysis using DESeq2.

I have three samples of different time points without replicates. I want to check the genes whose expression level changes over time.

I have studied time series analysis but I know that this analysis requires a comparison target such as control (untreated vs treated). I have control samples with replicates but these are not samples of different time points.

Is there any way to analyze using these continuous variables? Or Is there any commendable method of analysis using DESeq2?

Thank you in advance.

deseq2 • 73 views
ADD COMMENTlink modified 6 weeks ago by Michael Love24k • written 6 weeks ago by snu_jh0
Answer: Comparison of samples of different time points using DESeq2.
0
gravatar for Michael Love
6 weeks ago by
Michael Love24k
United States
Michael Love24k wrote:

The easiest way to get help is to fully describe your dataset. How many time points? How many control samples? These details matter in what we recommend.

ADD COMMENTlink written 6 weeks ago by Michael Love24k

Thank you for your prompt reply. I'm sorry I couldn't elaborate on my dataset.

We obtained RNA from three tumor samples with different volume sizes. We want to identify genes whose expression levels change when the tumor grows. The control samples is just a non-tumor samples.

I also know that my dataset is not good for analyzing with deseq2. But is there any way you can recommend it?

ADD REPLYlink written 6 weeks ago by snu_jh0

So you have 4 samples? I'm sorry, I'm still not certain your experimental design and sample size. How many volumes do you have? Is the volume per tumor sample the same? Are the tumors from different donors? Please post any relevant variables like this:

tumor, volume, donor
1,     15,     1
...
ADD REPLYlink written 6 weeks ago by Michael Love24k
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