Significance level of each variable used in the model

Question

[rthapa]

Hi,

I want to use two factorial model (two genotypes and two level of treatments) for analysis using DESEQ2. I want to see the interaction terms and main effects separately. I want to check if the gene expression is affected by treatment only or if the gene expression is effected by genotype only or if the gene expression is affected by treatment in genotype dependent manner. This may be a naive question.

Could anyone help me with this?

Thanks

Answer 1

[Kevin Blighe]

The DESeq2 vignette is the one and only answer. Happy reading: http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

Kevin