Design in DESEQ2

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3.5 years ago

hydrobeanz ▴ 10

Greetings, I have RNA-seq data need to be analyzed, How to do? I have two groups, one disease one no disease. Within each group, they received treatments of treatment A, B, C, D. This is all in one column in MetaData table (DiseaseTreatment), like NoDiseaseA, DiseaseA, NoDiseaseC, DiseaseC etc etc. How do I compared within DESEQ2 design? I want to compare NoDiseaseA-D to DiseaseA-C, and NoDisease overall to Disease overall.

dds <- DESeqDataSetFromMatrix(countData=mydata, colData=MetaData, design=~DiseaseTreatment)

then do: compare1 <- results(dds, contrast=c("DiseaseTreatment","NoDiseaseA", "DiseaseA"), independentFiltering=TRUE, alpha=0.05)

Is that right?

Many thanks.

RNA-Seq R • 606 views

ADD COMMENT • link updated 3.5 years ago by Kevin Blighe 87k • written 3.5 years ago by hydrobeanz ▴ 10

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I do not mean to sound harsh, but please go through the DESeq2 vignette:

https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

Biostar

ADD REPLY • link 3.5 years ago by Kevin Blighe 87k

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