RNAseq analysis on serial sample

Question

[Lakshmi]

Hi all,

I am new to RNA-seq analysis. I have data from RNA-seq performed on serial samples (before treatment, after treatment 1, after treatment 2) from 3 biological replicates (3 different patients). I was able to use DESeq2 in order to obtain the top differentially expressed gene sets. Since patients samples can be highly heterogeneous, I would also like to analyze the serial samples from each patient individually only for exploratory purpose. What is the best way to do that?

[Buffo]

Since patients samples can be highly heterogeneous

Have you analyzed that? How different/divergent they are? You can plot a PCA from your normalized raw counts to visualize it.

[Lakshmi]

I was hoping that the samples would align based on clinical response, but the samples group by biological sample.

[Ram]

Couldn't you use 2 grouping variables and results(..., contrast = ) based on what you need?

[Mahdiar Sadeghi]

ImpulseDE is a good way of analyzing time series samples. It gives you the genes that are going down, up or having a transient response.