Hi all

I have dataset of RNA-Seq data 3 different tissue and sequenced same time each individual has WT and KO data wanted differential gene expression tried read all question regarding design matrix still I am unable create design matrix any one please help me with it

I wanted generate DEG for tissue1 WT vs KO, tissue2 WT vs KO, tissue2 WT vs KO

     Cells  Type
    tissue1      WT
    tissue1      WT
    tissue1  WT
    tissue1      KO
    tissue1      KO
    tissue1      KO
    tissue2      WT
    tissue2      WT
    tissue2      KO
    tissue2      KO
    tissue3      WT
    tissue3  WT
    tissue3      KO
    tissue3      KO

for this kind of analysis I have to individually tissue wise I have to generate DEG? Please suggest me

#I tried using below design 

model.matrix(~ Cells + Cells:Type, data)

I think you are making this more complicated than it needs to be. I think you should follow the vignettes suggestion for what to do that isn't interactions.

https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions

Though if these are really much different tissues, I think it might be justifiable to make three different DESeq objects instead. You might not gain much by combining three very different tissues together.