making metadata file for differential gene expression analysis
I have RNAseq data from patients from 2 time points (before and after treatment) and want to do gene expression analysis comparing 2 time points.
if I want to use DESeq2, how should I make my metadata.csv file which will be used for differential gene expression analysis.
normally I make the metadata.csv file like this:
SampleID Condition
patent1-1 T1
patent1-2 T2
patent2-1 T1
patent2-2 T2
patent3-1 T1
patent3-2 T2
patent4-1 T1
patent4-2 T2
and at the end I will get fold change and p-values. how I should make this file for my data to compare 2 time points? shall I do it per individual or include all patients in the same metadata.csv file?
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You need to create a column patient, and then create a design
~ Patient + Condition