DESeq2 design for time series and control-treated groups
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T.RU • 0
@78148fe6
Last seen 11 months ago
Netherlands

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

DESeq2 • 319 views
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@mikelove
Last seen 12 hours ago
United States

For issues with setting up the statistical design, I recommend consulting with a local statistician. I have to reserve my time on the support site to software-related questions.

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