I am working with a RNASeq data from an Arabidopsis experiment. The plants have been subjected to nitric oxide treatment for 3 hours and for 8 hours. I would like to find differentialy modulated genes not only in the classic between 2 comparison but also at any time in one test, following the section "3.3.3 Treatment effects over all times" of edgeR user guide.
The design of the experiment is 3 biological replicates for each of the 3 samples:
I managed to compare samples at 3 hours with control (3h vs ctrl) and samples at 8 the hour treatment against control (8h vs ctrl); now I'd like to make a whole comparison to find genes responding to the treatment any time in a single test.
I am using edgeR.
This is the code I am using:
targets <- is the table above
design <- model.matrix(~Time, data=targets)
fit <- glmFit(y, design)
lrt <- glmLRT(fit, coef=2)
logFC logCPM LR PValue FDR
AT2G33270 1.3171504 4.287261 1136.0571 4.810643e-249 1.616472e-244
AT3G03270 0.9024100 8.335613 1116.2615 9.650825e-245 1.621435e-240
AT5G58840 1.1536560 4.831535 1108.5933 4.479132e-243 5.016927e-239
AT1G01460 1.8124852 3.853430 1079.3572 1.012809e-236 8.508099e-233
AT1G13480 1.3325911 5.177147 1062.6741 4.281367e-233 2.877250e-229
AT2G35730 1.1750776 5.391916 952.5724 3.660705e-209 2.050117e-205
AT4G02650 1.6227408 4.214342 913.3378 1.236992e-200 5.937916e-197
AT4G26470 0.9443015 4.350554 911.2471 3.522495e-200 1.479536e-196
AT2G02340 1.7263559 3.112108 890.8545 9.548953e-196 3.565155e-192
AT1G70440 1.6371184 5.024619 882.3160 6.857418e-194 2.304230e-190
Can you please tell me if this is correct (and in your opinion if it makes sense)?
Thanks a lot