[BioC] blue fuse output and limma

marchiem at libero.it marchiem at libero.it
Tue Aug 3 20:34:34 CEST 2004


Hello everybody,
we are evaluating a new image analysis software called Blue Fuse that uses a Bayesian approach to estimate the background. The outputs per each channell of this software are values with the background already subtracted.
How can I read in these output in BioC, specifically in limma?

I've used read.maimages and I've specified the columns just for foreground signal and I put NULL for the background:
RGblue<-read.maimages(files3,columns=list(Rf="AMPCH2",Gf="AMPCH1",Rb=NULL,Gb=NULL))

but I received this error message:

Error in "[<-"(`*tmp*`, , i, value = structure(list(), .Names = character(0), row.names = c("1",  : 
        nothing to replace with

I do apologies but I'm not yet confident in R so I can't understand how to solve the problem...

Maybe should I create another text file with two columns more for the background and put zero in them?

Does anyone know how to read this kind of data?

Thanks in advance and sorry again if I made some trivial mistakes.
Regards.

Emanuele



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