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T.RU • 0@78148fe6
Last seen 1 day ago
I am new at DESeq2 and trying to desing matrix to get DEGs. Basically, I need number of DEGs based on compare control/treated groups each time points.
dds <- DESeqDataSetFromMatrix(countData = round(counts_data), colData = colData, design = ~time + Compound_name + time:Compound_name ) dds<- DESeq(dds, test="LRT", reduced = ~ Compound_name + time)
I am confused how to design constrast.
a2_c <- results(dds, list(c( "timetime2.Compound_nameC" )), alpha = 0.1) a4_c <- results(dds, list(c( "timetime4.Compound_nameC" )), alpha = 0.1)
Are they DEGs on different time points which compared with control group at that time points? Thank you