DESeq2 for time series and control-treated groups
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Entering edit mode
15 months ago
t.ru ▴ 20

Hi,

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.

I tried

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

log2foldchange DESeq2 • 356 views
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