[BioC] limma design matrix with common reference

[michael watson (IAH-C)]

Hi Ron

When using limma I always fit the coefficients to a (normalised) MAList
object.  However, the documentation for lmFit() states:

Fit linear model for each gene given a series of arrays

lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation=0.75,w
eights=NULL,method="ls",...) 

object: object of class 'numeric', 'matrix', 'MAList', 'marrayNorm',
          'exprSet' or 'PLMset' containing log-ratios or log-values of
          expression for a series of microarrays

So lmFit() is basically a generic function which fits a linear model for
each gene based on *some data*, and so passing it an RGList is valid if
the RGList values are the data you want to use to fit linear models.
Note however that the docs do insist on either log-ratios or log-values.
It's definitely not a mistake to use an MAList object though, so go
right ahead.

Mick

-----Original Message-----
From: Ron Ophir [mailto:ron.ophir at weizmann.ac.il] 
Sent: 16 November 2004 09:16
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] limma design matrix with common reference


Hi,
I am analyze two color experiment with a common reference. It is a two
factor experiment with the following targets :
Cy3	Cy5
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IE	Control
EE	Control
EL	Control
IE	Control
IL	Control
EE	Control
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IL	Control
EE	Control
EL	Control
EL	Control
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IE	Control
EE	Control
EL	Control
where the first I/E is thetreatment factor and the second E/L is the
time factor. after preparing a design matrix with the argument
ref="Control" I tried to fit above coefficients.
>From limma userguide chapter 9.3 Common Reference Designs it is
suggested to fit the coefficients on RGList object:
fit <- lmFit(RG, design)
when I tried this I got an error message
Error in array(x, c(length(x), 1), if (!is.null(names(x)))
list(names(x),  : 
        dim<- : dims [product 362880] do not match the length of object
[8] It seems to me that it is more reasonable to fit the coefficients on
normalized dat and indeed when I trried to fit it on MAList object all
went well. Is it it a mistake to fit the coefficient on MAList object?
Ron

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