In a RNA seq project, samples for RNA extraction were collected from a split split plot design. Can we use DEseq2 for differential expression analysis for this type of data by taking into account the split split plot experimental design of data?
If not, which software would work best for this type of data.
Thanks!
DESeq2 allows for multi-factor analysis which is specified using the design formula within one of the constructor functions (such as DESeqDataSetFromMatrix). I would start with the vignette and see whether any of the examples there are suitable for your experimental design: http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#multi-factor-designs
Failing that, you can construct a fixed-effect term formula using the standard R syntax and see if DESeq2 accepts it (https://cran.r-project.org/doc/manuals/r-release/R-intro.html#Statistical-models-in-R).
Failing that, the authors of DESeq2 are quite responsive on their Bioconductor forum so you could always post a question there with the specifics of your dataset (https://support.bioconductor.org/).
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