Hi I am a newbie in RNA seq any help will be deeply appreciated. i have 100 cases and 100 controls for each case and each control i have four different cell type and each cell type will be treated with two chemical (so 4x2x2 possible situation). I want to check the DE between cases and controls, between cell types and between treatment and I have pretty much no idea where to start. so far I came to conclusion that using kallisto is probably a good option for expression quantification and as it doesn't work with DESeq i thought maybe sleuth can be used for DE analysis but I'm not sure if I'm right. I'll be grateful if you can explain briefly how so many groups can be compared trustable.