[BioC] Spotted array analysis

[Jean Yee Hwa Yang]

Hi Ron,

By default, M values are calculated as log(R/G) base 2.  If you have a
simple A vs B comparisons, here is a couple of options:

E.g. Assming you have 5 replicated experiment of A vs B.  Slides 1,2,4
were dye-swapped.

Option A) 

M <- maM(data) ## Extract M values

## Flip the M according to dye swap experiments

newM <-  sweep(M, 2, c(-1,-1,1, 1, -1), FUN="*")

## The vector of -1 and 1 indicate the experiments that were dye swaped.

Option B)

Uses lm.series for a linear model analysis. Input the dye swap
information as your design matrix

library(limma)
fit <- lm.series(maM(data), design=c(-1,-1,1,1,-1))

Cheers

Jean

On Thu, 26 Jun 2003, Ron Ophir wrote:

> Dear group members, I working with marrayXXX packages on genepix file.
> I wonder which channel is used as a reference, Green or Red, when the
> maNorm() function generates the "maM" matrix. Does M is log(R/G) or
> vise versa. I'm asking that because I analyze a dye swap experiment
> and I realize that I have to swap my self the reference for further
> analysis. I there a dye swap normalization function that does it
> automatically? Thanks in advance, Ron
> 
> Ron Ophir, Ph.D.
> Bioinformatician,
> Biological Services
> Weizmann Institute of Science
> POB 26
> Rehovot 76100
> Israel
> e-mail: Ron.Ophir at weizmann.ac.il
> Phone: 972-8-9342614
> Fax:972-8-9344113
> 
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