[BioC] Exact structure of RGList object (limma)

[Marcus Davy]

The Limma class "RGList" is a list with elements;

> names(RG)
[1] "R"       "G"       "Rb"      "Gb"      "weights" "targets" "genes" "printer"

R  - p x n matrix of red foreground intensities  (p spots/genes, n slides)
G  - p x n matrix of red foreground intensities
Rb  - p x n matrix of red background intensities
Gb - p x n matrix of red background intensities
weights - optional p x n matrix of spot weights
targets - auxillary cy3/cy5 mapping and/or filenames
genes - p x 5  matrix of gal mappings (usually)
printer - list of grid/spot row/column layout

You can construct one like this;

library(limma)

RG <-  new("RGList")
RG$weights <- matrix(...) # Appropriate matrix of spot flags/weights
RG$targets <- readTargets(...) # targets from tab delimited text file
RG$genes <- readGAL(...) # GAL text file information or from matrix(...)
RG$printer <- getLayout(RG$genes)
RG$R <- matrix(...)      # Repeat for G,Rb,Rg

You can add other auxilary information you think appropriate into the list.

Other option is to modify read.maimages(...) to work for your input files.

Marcus



>>> "Ken Termiso" <jerk_alert at hotmail.com> 20/06/2005 9:19:09 p.m. >>>
Hi all,

I am trying to take data from a scanner that is not part of the "core" group 
supported by limma, and create an RGList object from it, using the minimal 
components as defined in the limma docs. I've read in the CSV file and 
isolated the green and red F/G and B/G data for each chip, but what is 
unclear in the docs is the format that they need to be in...

In other words, is the order of slots/list components in the RGList object 
R1, G1, Rb1, Gb1...R1n, G1n, Rbn, Gbn for each chip, or is it R1...Rn, 
G1...Gn, Rb1...Rn, Gb1...Gbn (where n is the number of chips)?

Thanks in advance,
Ken

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