[BioC] LIMMA ignoring background

[Marcus Davy]

there are several options, 
you could modify read.maimages so that it can read in only Rf Gf, you could read in the Rb and Gb information as the foreground information aswell and remove it afterwards from the list elements of the RGList,
e.g. for GenePix, read.maimages(files[1], "genepix", columns= list(Rf = "F635 Mean", Gf = "F532 Mean", Rb = "F635 Mean", Gb = "F532 Mean")), 
or you could generate an RGList from scratch populating it with you data loaded into R using something like scan or read.table.

e.g.
library(limma) 

RG <- new("RGList")
# Two arrays, unrealistic data...
RG$R <- matrix(2^rnorm(8*4*20*20*2), nc=2)
RG$G <- matrix(2^rnorm(8*4*20*20*2), nc=2)

RG$printer <- list(ngrid.r=8, ngrid.c=4, nspot.r=20, nspot.c=20)
RG$printer <- structure(printer, class = "PrintLayout")

MA <- normalizeWithinArrays(RG,  method = "printtiploess", bc.method="none")

design <- rep(1,2)
fit <- lmFit(MA, design)
fit <- eBayes(fit)
topTable(fit, adjust.method="fdr")

You can populate exprSets and marrayRaw Class objects the same way using appropriate accessor methods.

Marcus

Marcus Davy
Bioinformatics
>>> Guoneng Zhong <guoneng.zhong at yale.edu> 05/03/05 8:39 AM >>>

Hi,

I have two-channel image result files that don't have background information,
just median and mean intensity readings.  But read.maimages requires that I
provide Rb, Rf, Gb, Gf values, and I don't have the Rb and Gb values.  How do I
make the analysis ignore those columns?  I am doing a simple lmFit and topTable.

THanks!
G

-- 

Systems Programmer
Yale Center for Medical Informatics
fax: 203-737-5708

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