[BioC] Error creating marrayInfo

[Jean Yee Hwa Yang]

Hi Dave,

Please test the following:

mydata.raw<-read.marrayRaw(fnames, path=NULL, name.Gf = "ch2 Intensity", 
name.Gb = "ch2 Background", name.Rf = "ch1 Intensity", name.Rb = "ch1
Background", skip = 12331)
maLayout(mydata.raw) <- mydata.layout
maGnames(mydata.raw) <- mydata.names
class(samples)
maTargets(mydata.raw) <- samples

to help me figure out why you get that error.  Basically, the output did
show that you have read in all the information but was having problems
assigning the "maTarget" slot in "mydata.raw" with the R object "samples".

> Why do I get this error? and what does the warning mean?
> We have each oligonucleotide sequence spotted two times on the chip. 
> How does the function handle duplicate spots?

The function read.marrayRaw simply reads in the data into R.  Currently we
are working on extending the class sturcture to include dpulicate /
replicate spots information.  You might like to take a look at the package
limma and the doc
http://bioinf.wehi.edu.au/limma/library/limma/html/00Index.html 
in particular the section linear models and the function gls.series
http://bioinf.wehi.edu.au/limma/library/limma/html/5linearmodels.html
which handels duplicate spots.

Cheers

Jean