Hi I am trying to analyze a dataset with a design quite like the dataset in the "airway" package.
but I am not sure I understood the differential analysis given as an example.
dds <- DESeq(dds)by doing this, i guess we could get all the differentially expressed genes (DEG) list of all the cells under different conditions
differentially expressed genes in N61311 (untrt vs trt) +
differentially expressed genes in other cell lines (untrt vs trt)
but how could we get the DEG of one cell lines under different conditions, i.g. N61311 (untrt vs txt) only?
I guess I need to use the "contrast" argument, but somehow I felt confused when reading the example,
results(dds, contrast=c("cell", "N061011", "N61311"))
it seems that "contrast" argument tried to compare two cell lines without specify which conditions (each cell lines have two conditions untrt vs trt,as far as I could tell. ) so what is "contrast" argument trying to compare, anyway?
Back to my own purpose, if I want to get DEGs between N61311 (untrt vs trt), what should I do?