Comparison between treatment timepoints in a single timeseries (control is first timepoint)
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Jigyasa • 0
Last seen 6 days ago


Thank you for a great resource! I am learning how to use DESEQ2 on time-series and I would like to get advice if my analysis is statistically "correct".

I have a single time-series i.e. the first time point is the control (t=-1) and the treatment starts from the second timepoint onwards (t=0). I have total of 8 timepoints of treatment (t=0, 1, 2, 3, 4, 5, 6, 7).

I want to compare each treatment timepoint with the control, and each treatment timepoint with the other. I am able to extract out DESeq results using the following code.

ddsMat <- DESeqDataSetFromMatrix(countData = countdata2,
                                 colData = metadata2,
                                 design = ~ Time)
ddsMat <- DESeq(ddsMat)

#output of each timepoint with "-1"
res_1 <-, name="Time_0_vs_.1", test="Wald",alpha=0.05,pAdjustMethod = "BH",format="DataFrame"))
res_2 <-, name="Time_1_vs_.1", test="Wald",alpha=0.05,pAdjustMethod = "BH",format="DataFrame"))

#condition2-output of each timepoint with the one before-
res2 <-, contrast=c("Time","1","0"),test="Wald",alpha=0.05,pAdjustMethod = "BH"))

I am interested in comparing res_1 and res_2, and found search results suggesting using ANOVA to compare these time points. When I examine res2 (called as Time_0_vs_1) for certain genes, I find that their log2FoldChange value lie between res_1 (called as Time_0_vs_-1) and res_2 (called as Time_1_vs_-1). Any suggestions on how to proceed?


DESeq2 single-timeseries TimeSeriesExperiment • 106 views
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Last seen 4 days ago
United States

I don't follow the problem here. The LFCs make sense to me.


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