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.
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).
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.
Check out this tutorials,
Instead of DESeq you try DESeq2.
I would suggest you to learn and understand the fundamentals of differential gene expression(DGE). Try to compile the following first :
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.
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