Limma time course with several conditions
1
0
Entering edit mode
rina ▴ 20
@rina-16738
Last seen 5 weeks ago
France

I have RNA-Seq, time series data from six conditions and five time points (i.e. 1h, 2h, 12h,24h, 48h). The conditions are the following:

WT (as Control)

Mut1

Mut2

Mut3

Mut1+2

Mut1+3

I want to run a differential analysis per time point using limma, using the WT as a control in each respective time point.

My design matrix is specified by

design <- model.matrix(~ 0 + fac)

where fac is a factor combining Mutant_Timepoint (Mut1_1h, Mut1_2h, ... , Mut1+3_24h, Mut1+3_48h)

Would there be any difference between using limma/voom with time series and the Time course section in limma's users guide? If yes, which one would be the most appropriate?

Thank you in advance for the help.

limma • 150 views
ADD COMMENT
0
Entering edit mode

Do you have replicate samples at each condition and time point?

ADD REPLY
0
Entering edit mode

Yes, I have three replicates per condition and time point, including for the control.

ADD REPLY
0
Entering edit mode
@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

You are free to make whichever comparisons are most of interest to your scientific study. Obviously, comparing conditions for each respective time will give different results than you would get by comparing time points for each condition, but it depends on what is of interest to you. You could even do both.

ADD COMMENT

Login before adding your answer.

Traffic: 460 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6