Question: Time-series Differential Expression Analysis
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gravatar for indrik.wijaya
3 months ago by
indrik.wijaya0 wrote:

Hi, I have a time-series data (7 time points & 2 replicates) and want to perform differential expression analysis. I am still new to this field and would like to find out more how to go about doing this. What I have thought of so far: 1) Finding differentially expressed genes between different time points (eg time 1 vs time 2, time 2 vs time 3, etc) 2) Finding differentially expressed genes across all the different time points

Are these 2 approaches correct or if not, how should I improve this?

And since DE tools such as edgeR and DESeq2 require design matrix as the input, may I know how to create the design matrix for the analysis I intend to do? Thank you!

ADD COMMENTlink modified 3 months ago by kristoffer.vittingseerup1.6k • written 3 months ago by indrik.wijaya0

Please read the DESeq2 manual about time series and visit/search the Bioconductor support page, e.g. here as there are plenty of questions on time series answered by the authors of the above-mentioned tools.

ADD REPLYlink written 3 months ago by ATpoint14k

Thank you for the help and link!

ADD REPLYlink written 3 months ago by indrik.wijaya0
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gravatar for kristoffer.vittingseerup
3 months ago by
European Union
kristoffer.vittingseerup1.6k wrote:

From your options I would go with option 2 since that will allow you to controle the false discovery rate (FDR).

But there is actually a third option: Stagewise FDR correction where you use the option 2 as a "screeening state" and then use the option 1 in a "validation stage". Such functionality is described in this article and implemented in the bioconductor stageR r-package. Take a look at this section of the vignette.

ADD COMMENTlink written 3 months ago by kristoffer.vittingseerup1.6k

Thank you, I will take a look at this method!

ADD REPLYlink written 3 months ago by indrik.wijaya0
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