I have some doubts when i'm running LRT
This is my condition data-frame small subset
dput(head(metadata,18))
structure(list(FAB = structure(c(1L, 1L, 1L, 1L, 6L, 2L, 6L,
4L, 3L, 5L, 7L, 3L, 2L, 7L, 6L, 2L, 6L, 2L), .Label = c("C",
"M0", "M1", "M2", "M3", "M4", "M5"), class = "factor")), row.names = c("H1",
"H2", "H3", "H4", "TCGA-AB-2856", "TCGA-AB-2849", "TCGA-AB-2971",
"TCGA-AB-2930", "TCGA-AB-2891", "TCGA-AB-2872", "TCGA-AB-2851",
"TCGA-AB-3011", "TCGA-AB-2949", "TCGA-AB-2981", "TCGA-AB-2965",
"TCGA-AB-2822", "TCGA-AB-2828", "TCGA-AB-2959"), class = "data.frame")
Now I m running LRT on this. In pairwise comparison condition I can set the reference level as such
coldata$condition<- relevel(coldata$condition, ref = "H") where H` is my control set with whom I compare all other factors.
Now if I have to do the same with LRT is it correct to set the reference level?
Second doubt
If i have to run LRT using different reference level how to do that?
dds <- DESeq(dds, reduced=~condition, test="LRT")
dds_lrt <- DESeq(dds, test="LRT", reduced = ~ 1)
