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Old 11-05-2015, 02:26 AM   #1
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 149
Default DESeq2 dynamics in a timecourse experiment

dear all,

we are trying to analyse a time-course data set of several time-point with replica. we're looking for genes which are changing across all TP as well as genes with a difference on a pair-wise comparison between two time points.

My questions regards the sensitivity of the dynamics in the analysis of DSeq2.
Identifying significant changes when considering multiple time-points isn't as simple as a consistent change over all time-points continuously, because a gene can be high at 1 or 2 time-points and off at the rest, and that is a significant biological difference.

my question is therefore does DESeq2 timecourse model design is able to identify genes which are going up and down over multiple time-points in my time course experiments

for example, if I have a gene which goes high up after 1h, than normalized and than again go down after 24h, will deseq2 be able to identify this genes as a significantly deregulated genes over all time-points?
Do I need to check for all coefficients to get a complete overview of the genes changed over time?

thanks

Assa
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