Question: Time-series Differential Expression Analysis
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gravatar for indrik.wijaya
19 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 19 months ago by kristoffer.vittingseerup3.3k • written 19 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 19 months ago by ATpoint36k

Thank you for the help and link!

ADD REPLYlink written 19 months ago by indrik.wijaya0

Hi could you please tell how you got around this? I have a similar dataset.

ADD REPLYlink written 7 months ago by arjundvas0

Please open a new question with sufficient details to answer your question.

ADD REPLYlink written 7 months ago by ATpoint36k
0
gravatar for kristoffer.vittingseerup
19 months ago by
European Union
kristoffer.vittingseerup3.3k 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 19 months ago by kristoffer.vittingseerup3.3k

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

ADD REPLYlink written 19 months ago by indrik.wijaya0
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