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Hello Sally, You should try the following commands: myfun <- function(x) as.numeric(x$Flag ==0) RG <- read.imagene(filenames$target, wt.fun=myfun) I hope it helps. Good luck. Leonardo ----- Original Message ----- From: "Sally" <sagoldes@shaw.ca> To: <bioconductor at="" stat.math.ethz.ch=""> Sent: Tuesday, November 06, 2007 9:36 PM Subject: Re: [BioC] Limma and Imagene flags > >From reading the Limma User's Guide it says that a flag value of 0 means > >that Limma considers this a "bad spot" and removes data flagged 0 from > >subsequent preprocessing. But in Imagene a flag value of 0 means that > >this is a "good spot". How do you get around this? > > > Sally > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor