Question: Detection of DE genes among different tissues of an organism during time - RNA seq
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4.4 years ago by
statfa530 wrote:

Hi there!

I've been researching but haven't found any result yet. Do you think there is some (statistical) methods designed for detecting Differentially Expressed Genes among different tissues in an organism during time? I mean do you think it is possible to find out what genes are expressed differentially in different tissues in time series RNA-seq data? It is like a factorial design (study) in which we have "time" and "different tissues" as possible factors that may influence expression of genes. If there is no direct method to do so, what do you recommend to solve such problems?

Thank you

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by statfa530

Look into the limma package of R from the Bioconductor project

ADD REPLYlink written 4.4 years ago by Lluís R.970

limma ,deseq2 are all able to perform this , in addition you can also look at dexus

You need to make the proper contrast to make the actual design you wish to make for comparisons w.r.t to a design that will have all variables but not the comparisons.

DESEQ2 time coure

limma time course . starts from page 46

Check some examples here

ADD REPLYlink written 4.4 years ago by ivivek_ngs5.0k

Thank you so much for the information!

ADD REPLYlink written 4.4 years ago by statfa530

Thanks a lot! I'm currently reading into it.

ADD REPLYlink written 4.4 years ago by statfa530
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