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=N ULL,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

At 04:34 AM 4/08/2004, marchiem\@libero\.it wrote: >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)) The recommended way to read BlueFuse data into limma is RG <- read.maimages(files,columns=list(Rf="AMPCH2",Gf="AMPCH1",Rb="AMPCH2",G b="AMPCH1")) RG <- backgroundCorrect(RG, method="none") This question has been previously addressed on this mail list, see: https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-February/003 674.html BlueFuse also has a confidence value column, although I am not sure of the precise name of this column. (There isn't any online documentation.) To make use of this column, you could include a 'wt.fun' argument to read.maimages(), for example: mywtfun <- function(x) x[,"CONFIDENCE"] RG <- read.maimages(files,columns=list(Rf="AMPCH2",Gf="AMPCH1",Rb="AMPCH2",G b="AMPCH1"),wt.fun=mywtfun) where "CONFIDENCE" is the name of the confidence value column. Gordon >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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor