Differential gene expression using R studio

Question

[rachana.cdri]

Hello everyone,

I am new to r-studio and I have to do differential gene expression analysis for my RNA seq data. Please tell me how should I start.I already have read counts for my samples.

Thank you

[cpad0112]

Read about rnaseq here by University of Oregan. http://rnaseq.uoregon.edu/. Once RNAseq fundamentals are clear, try to reproduce this workflow as you are looking for differential gene expression: https://www.bioconductor.org/help/workflows/rnaseqGene/. R studio, as many people said here, is a R front end.

Could you update us with the method of obtaining read counts? (for eg featurecounts or htseq or any other tool).

Answer 1

[Ram]

RStudio is an interface. You're looking for software written in R (called packages) that help you with DE analysis. Packages such as DESeq2 and edgeR might be a good place to start.

Answer 2

[EagleEye]

Check out this tutorials,

http://www.gettinggeneticsdone.com/2012/09/deseq-vs-edger-comparison.html

OR

https://web.stanford.edu/class/bios221/labs/rnaseq/lab_4_rnaseq.html

Instead of DESeq you try DESeq2.

Answer 3

[lakhujanivijay]

Dear Rachana,

I would suggest you to learn and understand the fundamentals of differential gene expression(DGE). Try to compile the following first :

1. What is the objective of your study?
2. What do you have as your data set, experimental setup, replciates, species in question, source of samples etc.
3. Fundamentals of DGE - mapping, raw read counts, FPKM, RPKM or TPM.

A nice paper could be found here

Then, finally decide the appropriate tool; though all of them can more or less perform the basic analysis for you.