[BioC] LIMMA: MA, design, and contrasts

[Tiandao Li]

Hello Jenny,

I created a composite design matrix with some common reference arrays and 
arrays from some loop designs, such as loop design 1 and loop design 2. I 
have a big MA with all normalized arrays, and a big contrast matrix to 
find the differentially expressed genes in different treatments only 
existed in loop design 1. Or, I can build a small MA, a small design 
matrix using the same reference, and contrast matrix for some contrasts 
only for arrays in loop design 1. Which way can I get more reliable 
result? Or I will get the same result.

Thanks,

Tiandao 


On Thu, 20 Sep 2007, Jenny Drnevich wrote:

Hi Tiandao,

A quick answer to your first question:

>corfit <- duplicateCorrelation(MA,design,ndups=4) # A slow computation!

The order of the arrays in the columns of MA **MUST** match the order 
of the arrays in the rows of design, else your design matrix is not 
correct for your MA object.


>2. I have one MA file including all my experiments, and also an all-in-one
>contrast matrix including different contrasts (related or un-related).
>Should I use this all-in-one contrast matrix for linear model to find the
>differentially expressed genes? This doesn't sound right. Or I use subset
>of MA for and only for related one or more contrasts, and use all-in-one
>MA only necessary. Which one is better?

I don't quite understand your second question... each contrast in 
your contrast matrix will be estimated separately using only those 
columns of MA that are indicated from the design matrix and the 
contrast matrix. Perhaps if you could explain your question in more 
detail with example code, we could better answer it.

Cheers,
Jenny



>Thanks in advance,
>
>Tiandao
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

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