RNA seq

Question

[Byonkesh]

Hi,

I have collected two types of kidney tissues - normal and disease. I have 3 biological replicates. RNA seq is done for this set up. I am stuck with the data analysis. I want to compare normal vs disease kidney tissue. When I think of averaging biological replicates for each tissue types, I find it a bit problematic because I want to capture the differentially expression gene data between the different tissue types in a biological replicates.

Additionally, organs in different humans are bound to be different due to various factors. Furthermore, I also want to compare the normal tissue of different biological replicates.

Any suggestion please?

[ATpoint]

What is the question? I assume you googled 'differential RNA-seq' and tried the obvious tools such as DESeq2 and limma?

[Istvan Albert]

there is no need to "average" anything, the point of replicates and RNA-Seq in general, is to measure the same thing several times and use tools designed to figure out whether the inter-replicate variability is larger than the intra-condition variation

Answer 1

[jv]

Don't try to reinvent the wheel. There are well established methods for performing differential expression testing. Start here https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html