Hello,

I am new at EdgeR. I have 6 RNA-Seq samples in different time points and I would like to find DE genes changes during developmental stages. my samples are 

sample 1 and 2 are biological replicates and so on...

How can I find the DE genes?

I am also interested to extract the list of genes goes up or down in all stages.

Could you please help me with this?

Thanks

Simon

Hi Simon,

It's better if you at least make a start on the analysis yourself, rather than asking us to provide it for you from start to finish. Have you tried reading the edgeR User's Guide? Your study is a fairly simple one with just 3 groups, so this is well covered in the Users Guide.

It would be helpful to know how far you've got already. Have you already aligned the RNA-seq reads to a reference genome? Have you obtained read counts for each gene? If so, have you managed to read them into R?