I am using the limma packages for the first time, and I need help with the modifyWeights function. I have about three years of experience with R programing, but this is the first time that I have run an analysis with a bioconductor package. I have included the code below. I know that this is not a reproducible example and I would gladly give any more information requested. I am trying to modify the weights of genes that I know are housekeeping genes (upweight). I can not get the modifyWeights function to work to save my life. The weights array is 6400, 6. The control status vector is 12800- that seems like only two of the arrays are being represented??????? I don't know what is wrong. Any help would be greatly appreciated thanks, Stephen Sefick library(limma) library(marray) library(convert) library(statmod) #read in targets file targets <- readTargets("targets.txt", row.names="Name") #weight everything with flags !cutoff=0! RG <- read.maimages(targets$FileName, source="genepix", wt.fun=wtflags(cutoff=-50 weight=0)) #read .gal file #remove extra tab in file a <- readGAL() b <- a[,-6] RG$genes<-b #spot types file spottypes <- readSpotTypes() RG$genes$Status <- controlStatus(spottypes, RG$genes) ##################CHANGE weighting for spot types##################### ###################################################################### multiply <- c(1,0,2,0,1,0,1,1,1) ###################################################################### ###################################################################### a <- unique(RG$genes$ID) status=RG$genes$Status w <- modifyWeights(RG$weights, RG$genes$Status, a, c(0, 1)) -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis