EBSeq-HMM on time-course of control-treated samples

[Tagnone]

Hi,

1- Is it possible to use EBSeq-HMM on HTSeq output? Based on the EBSeq-HMM vignette I would say yes, but need a confirmation from experts.

2- I have samples from 4 time-points, each time-point having control and treated conditions. I am interested in finding DEGs between conditions and time-points. Because the example used in the paper and the vignette does not really match my experimental setup, I want to ask if EBSeq-HMM would be appropriate for the vertical (based on treatment) and horizontal (time-point) comparisons simultaneously.

Thanks for your help.

[Ning Leng]

Hi,

Unfortunately, currently EBSeqHMM doesn't implement functions to
perform cross-condition analysis on time course data. Alternatively,
you may try to run EBSeq to detect DE genes between control/treatment
at each time point, then combine the results with the EBSeqHMM
identified genes that are changing along the time points.

hth,
Ning

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--
Ning Leng, Ph.D
Computational Biologist / Biostatistician
Regenerative Biology Laboratory
Morgridge Institute for Research

[Tagnon Missihoun]

Thank you for the quick feedback. Do you think that DESeq output of DEGs could be used as well?

[Ning Leng]

Yes I think that will be feasible too. Although I suspect the EBSeq
results and EBSeqHMM results will be more comparable, given that they
make similar model assumptions and the parameter estimation
implementations are similar.
Best,
Ning

[Tagnon Missihoun]

Thank you!