I am a newbie so sorry for asking a simple question. Can someone help me answer the following question, I spent many hours but stuck?
Thank you so much in advance for your help.
Here is my models:
model1.matrix( ~ Group + Gender + Group:Gender , data=X, contrasts.arg = lapply(data.frame(X[,sapply(data.frame(X), is.factor)]), contrasts, contrasts = FALSE))
model3.matrix( ~ Group:Gender , data=X, contrasts.arg = lapply(data.frame(X[,sapply(data.frame(X), is.factor)]), contrasts, contrasts = FALSE))
When I run the following code on the above models:
fit = lmFit(data, model) efit<-eBayes(fit) topTable(edit)
I get completely different answers for the "Group:Gender" when using model1.matrix Versus model3.matrix. The model3.matrix appears to be correct for "Group:Gender". Can someone show exactly how to fix model1.matrix so I get the same results for "Group:Gender" in model3.matrix
Here is my metadata:
Sample.ID TimePoint Group Gender 301 0 Group1 Female 302 0 Group1 Male 303 0 Placebo Female 304 0 Group1 Female 305 0 Group1 Female 306 0 Placebo Female 307 0 Group2 Female 308 0 Group2 Female 309 0 Group2 Female 310 0 Placebo Male 311 0 Group3 Female 312 0 Group3 Male 313 0 Group3 Female 314 0 Group2 Female 315 0 Placebo Male 316 0 Group2 Female 317 0 Group3 Male 318 0 Group2 Male 319 0 Placebo Male 320 0 Group1 Male ETC....