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Hi,
I have RNA seq data for 7 time points with 3 replicates each, I would like to mark genes that are differentially expressed at least at one of the time points.
The DESeq manual details about dealing with time series data that have two conditions.
In general I would like to have a figure like this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462286/figure/F1/ (figure B).
Kindly help.
Thank you
Hi,
I just have the time series, it is a developmental data set with three replicates for each stage.
Thank you for the link.
You can use a design of ~time, where time should be a factor, not a numeric variable:
class(dds$time)
And then you can use the following test:
This will produce p-values testing if the mean level is constant across all times (the null hypothesis). See ?results and the section in the vignette about the LRT for more details.