Question: Detect genes that moved up or down over time in the same way in multiple strains, DESeq2
0
gravatar for huganye
10 weeks ago by
huganye0
huganye0 wrote:

Hello Michael and community,

I am using DESeq2 to analyze a time course experiment. My time course experiment has only one (rather than two) group of samples, and I am interested in detecting genes that moved up or down over time in the same way among all samples.

The latest version of DESeq2 tutorial has shown a good example on how to test interaction term between samples and time points. However, there is no illustration on the case of identifying genes with same expression trends (linear or non-linear) over time among multiple samples.

Could anyone give a hint how to do it with DESeq2 or suggest any other robust test?

Thanks!

deseq2 • 73 views
ADD COMMENTlink modified 10 weeks ago by Michael Love22k • written 10 weeks ago by huganye0
Answer: Detect genes that moved up or down over time in the same way in multiple strains
3
gravatar for Michael Love
10 weeks ago by
Michael Love22k
United States
Michael Love22k wrote:

It sounds like you could transform the data to variance stabilize (e.g. vst), remove the mean per gene across samples, and then cluster the genes.

I don't have any code for this in the vignette or workflow, but it's pretty simple using base R to do this.

ADD COMMENTlink written 10 weeks ago by Michael Love22k
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