Hi there,
I have been given an RNA seq dataset of the raw counts, Ensembl ID and gene symbols in an excel spreadsheet. The experimental design is two groups (control v experimental), 6 time-points, 5 replicates per time point (therefore 60 samples in total).
My aim is to run differential expression analysis using EdgeR to see which genes have significantly changed in my experimental group vs my control.
I plan to run these sig. changed genes through EnrichR using “KEGG 2019 MOUSE” to produce pathways of interest.
I have been given some example code from a previous colleague to assist me, but this code assumes I'm using EnterezID rather than EnsembID which has made things trickier and confusing for me. This colleague has now left and there is nobody to help me. I have read the EdgeR user guide, searched all the questions on here, and tried to find tutorials online but I am still struggling.
Does anyone know where I can find any example code with a similar dataset that I can follow to help me run the analysis?
I am very new to RNA seq analysis (and R!) so would appreciate any help and guidance
As someone who also started looking at transcriptomics recently, I can highly recommend this tutorial series - https://diytranscriptomics.com/, depending on whether you are working with microarray or RNA-seq data (it is not clear from your post but I am guessing it is microarray) you might have to find entry points in the tutorial where you can fit your own analysis.
And to convert entrezID to ensemblID - you could do this with biomaRt library in R. To see how you can go about doing this in biomaRt you can use this post as a reference (Microarray - multiple probe-ids matching to the same gene symbol but different ensembl_gene_id), specifically the comment from user-bk11
Amazing, thank you! I'll give this a go
Hello,
To learn how to use edgeR, I recommend this methodological article
For annotation of expression matrix I use AnnotationHub.
Here are some functions I've written in R for expression matrix annotation.