Hello,

We am analyzing some RNASeq data from two different cell types, three condition (fhreshly isolated cells and stimulated cells for 90m or 4h). What we need is to identify those genes that are differentially expressed between the cell type tacking in account also the time factor. This because we are interested in those genes that are differentially expressed in at least one of the two time point after 0 (in at least one of the cell type) and, at the same time, they are differentially expressed also between the two cell types.
We plan to model the data with this formula:
 dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design = ~ Time + Cell + Time:Cell)
and than recover the results in this way:
 res1 <- results(dds, contrast=list(Cell1,Cell2))
 res2 <- results(dds, contrast=list("Time0.Cell1","Time0.Cell2"))
 res3 <- results(dds, contrast=list("Time90.Cell1","Time90.Cell2"))
 res4 <- results(dds, contrast=list("Time240.Cell1","Time240.Cell2"))
 res5 <- results(dds, contrast=list(c("Cell1","Time0.Cell1"), c("Cell2","Time0.Cell2")))
 res6 <- results(dds, contrast=list(c("Cell1","Time90.Cell1"), c("Cell2","Time90.Cell2")))
 res7 <- results(dds, contrast=list(c("Cell1","Time240.Cell1"), c("Cell2","Time240.Cell2")))

We understand the first 4 results table but we obtained exactly the same results from res 2 to 4 and res5 to 7. Furthermore we didn't obtain the results we need.

Is what we did correct? If not how we can obtain the file with the gene of our interest?
Thanks

Barbara and Francisco