Question: how to decide whether intercept term is necessary for GLM model or not
1
gravatar for illinois.ks
4.7 years ago by
illinois.ks140
Korea, Republic Of
illinois.ks140 wrote:

Hello,

 I have read several materials including the edgeR and GLM manual. I am wondering whether I need to add intercept into the mode.

I am reading the edgeRUserGuid maual..for example, suppose we have such data composing from 12 samples..

==============================

> targets
Sample Treat Time
1 Sample1 Placebo 0h
2 Sample2 Placebo 0h
3 Sample3 Placebo 1h
4 Sample4 Placebo 1h
5 Sample5 Placebo 2h
6 Sample6 Placebo 2h
7 Sample1 Drug 0h
8 Sample2 Drug 0h
9 Sample3 Drug 1h
10 Sample4 Drug 1h
11 Sample5 Drug 2h
12 Sample6 Drug 2h

========================================================

Two Design matrix looks like this.. 

> Group <- factor(paste(targets$Treat,targets$Time,sep="."))
> cbind(targets,Group=Group)

> design1 <- model.matrix(~0+Group)

> colnames(design1) 

[1] "GroupDrug.0h"    "GroupDrug.1h"    "GroupDrug.2h"    "GroupPlacebo.0h" "GroupPlacebo.1h" "GroupPlacebo.2h"

 

> fit1 <- glmFit(y, design1)

=========================================

> design2 <- model.matrix(~Treat + Treat:Time, data=targets)

colnames(design2)
[1] "(Intercept)" "TreatDrug"
[3] "TreatPlacebo:Time1h" "TreatDrug:Time1h"
[5] "TreatPlacebo:Time2h" "TreatDrug:Time2h"

> fit2 <- glmFit(y, design2)

==================================

What is the diffference for

glmLRT(fit1, coef=2)        VS.       glmLRT(fit2, coef=4)     ????????????????????

Are they testing the same thing, which find genes resposive  for Drug at time 1h...(compared to time 0).?????????????? If it is same, I think there is no reason for intercept term. If it is not, what is the difference for those tests?? 

===================================================

rna-seq • 3.7k views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 4.7 years ago by illinois.ks140
4
gravatar for Devon Ryan
4.7 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

They're in no way the same thing. Without an intercept, you're basically asking of a gene has signal above 0 in a particular group (i.e., glmLRT(fit1,coef=2) is unlikely to answer your biological question). If you want to compare (i.e., contrast) a number of the groups, such as GroupPlacebo.1h vs. GroupDrug.1h, then not having an intercept can make that a little easier.

I should note that times like this are when having taken a bit of linear algebra comes in quite handy. If you're affiliated with a university and have never taken linear algebra, I would highly recommend it. You'll find many statistical procedures (such as what a model matrix is actually doing) much simpler then.

ADD COMMENTlink written 4.7 years ago by Devon Ryan88k

thank you so much!!.. yes. i will try to find some extra material.. ;) 

ADD REPLYlink written 4.7 years ago by illinois.ks140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2580 users visited in the last hour