Entering edit mode
8.3 years ago
unique379
▴
120
Dear folks,
I would like to correct batch of my time course data but the problem is to design matrix for sva as input. So is there way to design matrix having two groups (WT and KO) along with four time points (1 month, 3 months, 12 months and 22 months) including their replicates ??
> wt.ko.edesign
time Time Group Replicates WT KO
F1WT5wks fiveWeeks 1 WT 1 1 0
F2WT5wks fiveWeeks 1 WT 1 1 0
F3WT5wks fiveWeeks 1 WT 1 1 0
F1WTY young 3 WT 2 1 0
F2WTY young 3 WT 2 1 0
F3WTY young 3 WT 2 1 0
F4WTY young 3 WT 2 1 0
F1WT1Y one_year 12 WT 3 1 0
F2WT1Y one_year 12 WT 3 1 0
F3WT1Y one_year 12 WT 3 1 0
F4WT1Y one_year 12 WT 3 1 0
F1WTOld Old 22 WT 4 1 0
F2WTOld Old 22 WT 4 1 0
F3WTOld Old 22 WT 4 1 0
F4WTOld Old 22 WT 4 1 0
F5WTOld Old 22 WT 4 1 0
F6WTOld Old 22 WT 4 1 0
F1KO5wks fiveWeeks 1 KO 5 0 1
F2KO5wks fiveWeeks 1 KO 5 0 1
F3KO5wks fiveWeeks 1 KO 5 0 1
F1KOY young 3 KO 6 0 1
F2KOY young 3 KO 6 0 1
F3KOY young 3 KO 6 0 1
F4KOY young 3 KO 6 0 1
F1KO1Y one_year 12 KO 7 0 1
F2KO1Y one_year 12 KO 7 0 1
F3KO1Y one_year 12 KO 7 0 1
F4KO1Y one_year 12 KO 7 0 1
F1KOOld Old 22 KO 8 0 1
F2KOOld Old 22 KO 8 0 1
F3KOOld Old 22 KO 8 0 1
F4KOOld Old 22 KO 8 0 1
F5KOOld Old 22 KO 8 0 1
F6KOOld Old 22 KO 8 0 1
I tried with :
ddsTC <- DESeqDataSetFromMatrix(countData=filtered, colData = wt.ko.edesign, design = ~Group + time +Group:time)
## Transfrom matrix in rlog
rld <- rlog(ddsTC,blind = TRUE)
dat <- as.matrix(assay(rld))
## design matrix for sva
mod <- model.matrix(~ Group + time + Group:time, colData(ddsTC))
## Run sva
sva_covariates <- sva(dat, mod, mod=NULL, n.sv=1)
But i am not sure whether i am doing right design matrix or should i only consider groups as :
mod <- model.matrix(~ Group, colData(ddsTC))
or Group and Time both as:
mod <- model.matrix(~ Group+ time, colData(ddsTC))
?? please help Thank you.