Hello,
I have RNASeq data from two conditions (control, treatment) each with 5 different time points 0d, 3d, 7d, 14d, 21d (each with two biological replicates). I see you your answer in this thread C: DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points to get the genes over the time between the condition (control vs treated) and just over the time (avg. all the time point of control and treated and get the genes over the time).
I'm looking four different set of genes...
1. genes over the time between/across the condition
2. just over the time
3. contrast of each time point between control vs treated
4. genes over the time but with in each individual condition ie. DE genes over the time in control separately and the genes over the time in treated separately
For the first question I see ~condition + time + condition:time as the design
dds <- DESeq(dds, reduced=~condition+time, test="LRT")
res <- results(dds)
second question design(dds) <- ~condition + time
dds <- DESeq(dds, reduced=~condition, test="LRT") res <- results(dds)
How would I do the one for my fourth question? over the time of genes in each condition separately
Please explain me what is the design matrix suppose to be used and the test (LRT or Wald)?
I'm thinking of use the matrix only with one condition of the data eg. all the time points of control data and use design(dds) <- ~ time
dds <- DESeq(dds, test="Wald")
One more question, please clarify me any difference of saying/calling DE genes *over the time and all the time point* here, what represents over the time (just DE genes at every time point)?
Here's my matrix. Thank you in advance.
Library Replicate group condition time
R76 A group1 control 0d
R85 B group1 control 0d
R77 A group2 control 3d
R86 B group2 control 3d
R79 A group3 control 7d
R88 B group3 control 7d
R81 A group4 control 14d
R90 B group4 control 14d
R83 A group5 control 21d
R92 B group5 control 21d
R76T A group1 treated 0d
R85T B group1 treated 0d
R78 A group6 treated 3d
R87 B group6 treated 3d
R80 A group7 treated 7d
R89 B group7 treated 7d
R82 A group8 treated 14d
R91 B group8 treated 14d
R84 A group9 treated 21d
R93 B group9 treated 21d
Thank you very much Michael. yes I will apply either of the model how the DE over the time across the condition or over the time of individual condition. wanted to know other possible scenario in time series.