[BioC] a question on creating model.matrix using limma

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Wed Jul 12 00:43:24 CEST 2006

Dear Dr. Smith and group, 

apologies for simple question. 

I have data with simple plan.  There are 8 samples (4
normal and 4 tumor). These tissue samples are from
different patients. No replicate experiments were
I wish to see genes differentially expressed between
Tumors and normals.

In such cases how can I create model.matrix

Following is taken from Limma manual:

design <- model.matrix(~ -1 +

my question: 
 1. what is '~ -1' is for?
 2. Will this work for my study structure. That means
I have only two types of RNA 1. tumor  and 2. Normal. 
design <- model.matrix(~ -1 +


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