Problem in defining groups from GSE in R

Question

[786]

Hi everyone!! I'm working on GSE24422 and GSE67297 and facing difficulty in defining groups. I just couldn't understand that how to define groups for these GSE's. Anyone can help me to get out of this situation??It will be very helpful for me.

[Mike]

First, please post your initial R code you tried. I think you are talking about sample and matrix design of your experiment, for this please refer limma package manual.

look at some previous post:

Limma Multiple Group Analysis

Limma analysis for multiple groups

Limma Contrast matrix

Though in GSE24422 data there are total 24 samples, including replicate (12*2). So the sample Id is your group, you can define as follow:

sample code:
  group <- factor(rep(c("Mixed_rep", "Mixed_Ins_rep", "Mixed_TNF_rep", "Mixed_TNF_Ins_rep", "Adip_rep", "Adip_Ins_rep", "Adip_TNF_rep", "Adip_TNF_Ins_rep", "Strom_rep", "Strom_Ins_rep", "Strom_TNF_rep", "Strom_TNF_Ins_rep"),each=2))
 design <- model.matrix(~0 +group)
 colnames(design) <- c("Mixed_rep", "Mixed_Ins_rep", "Mixed_TNF_rep", "Mixed_TNF_Ins_rep", "Adip_rep", "Adip_Ins_rep", "Adip_TNF_rep", "Adip_TNF_Ins_rep", "Strom_rep", "Strom_Ins_rep", "Strom_TNF_rep", "Strom_TNF_Ins_rep")

 fit <- lmFit(eset, design)
 contrast.matrix <- makeContrasts(Mixed_rep-Mixed_Ins_rep, levels=design)

[786]

Thank you so much. But what about GSE67297? In GSE67297 I want to compare subjects befor 10 days of cold acclimation and after 10 days of cold acclimation but unable to understand how make contrast.matrix. Can you please help me in this too??