Hi,
I want to add the two variables condition and treatment to my DESeqDataSet, and I thought I had succeeded:
> ddsHTSeq
class: DESeqDataSet
dim: 21680 11
exptData(0):
assays(1): counts
rownames(21680): scign000001 scign000002 ... scign021679 scign021680
rowData metadata column names(0):
colnames(11): R1D0B1 R1D2B1 ... R3DxB1 R3DzB1
colData names(2): condition treatment
I added four levels to condition and two levels to treatment and I am able to pull out DESeq results from the different levels of condition, but I can't pull out the results from treatment:
> resTreatment = results(ddsHTSeq, contrast=c("treatment", "cut", "uncut"))
Any ideas what I am doing wrong?
I want to add the two variables condition and treatment to my DESeqDataSet, and I thought I had succeeded:
> ddsHTSeq
class: DESeqDataSet
dim: 21680 11
exptData(0):
assays(1): counts
rownames(21680): scign000001 scign000002 ... scign021679 scign021680
rowData metadata column names(0):
colnames(11): R1D0B1 R1D2B1 ... R3DxB1 R3DzB1
colData names(2): condition treatment
I added four levels to condition and two levels to treatment and I am able to pull out DESeq results from the different levels of condition, but I can't pull out the results from treatment:
> resTreatment = results(ddsHTSeq, contrast=c("treatment", "cut", "uncut"))
Any ideas what I am doing wrong?
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