DESeq2 with temporal data and different treatments
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T.RU • 0
@78148fe6
Last seen 1 day ago
Netherlands

Hi,

I have 3 different compounds and one control groups with 7 different time points. I would like to run DESeq2 analyses and get differentially expressed genes with reference of the contol group


dds <-DESeqDataSetFromMatrix(countData = round(counts_data), colData = colData,
design = ~time + Compound_name + time:Compound_name )

dds$Compound_name <- relevel(dds$Compound_name, ref= '0.1 % DMSO')


However, I could not get the DEGs of compounds based on different time points since the results names return

 [1] "Intercept"                               "time"                                    "Compound_name_CD_vs_0.1...DMSO"       [4] "Compound_name_CS_vs_0.1...DMSO"   "Compound_name_TN_vs_0.1...DMSO"         "Compound_name_TM_vs_0.1...DMSO" [7] "time.Compound_nameCD"                  "time.Compound_nameCS"          "time.Compound_nameTN"                   10] "time.Compound_nameTM


(I couldnot put every variables names)

How can I reach the different time points by contrast?

Thanks

DESeq2 • 86 views
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For starters, spaces and a % in your coldata? That could be the problem.

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@mikelove
Last seen 1 day ago
United States

Sorry I don't have sufficient time for answering non-software related questions on the support site. I recommend consulting with a local statistician.