batch effect in RNA-Seq

Question

[ahmad]

Hello I am working on RAN-Seq ,I have question regarding Batch effect, how can get or be sure that I have batch effect?.

2- Is it mandatory to remove it from my count matrix before downstream differential gene expression expression?

3- Which package shall bed used with Deseq2 ? limma, RUVSeq, or SVA?? In my project I have 2 conditions each has 3 samples each sample is generated on different time or phase.

Thanks in advance

[ATpoint]

A good start is to diagnose if there is even a batch effect, using PCA for example. See the DESeq2 manual, or use my tutorial for inspiration: Basic normalization, batch correction and visualization of RNA-seq data

Answer 1

[Istvan Albert]

Generate a PCA plot for your data and investigate the effects.

That plot will let you evaluate the size of the batch effects relative to the size of the effects of the treatments/conditions.

You may or may not need to perform batch effect correction.

Answer 2

[swbarnes2]

I don't know that you could even detect, let alone correct batch effect between only 6 samples. Especially not if batch corresponds perfectly with sample.