Hi there I would like to generate a histogramof my data after normalision using oligo rma. See code below. library(oligo) celfiles <- list.celfiles("cel_files",full.names = T) twfs <- read.celfiles(celfiles) results <- rma(twfs) hist(results) The hist implementation in this instance takes the log2 of the expression set elements before making the plot. This is a problem since the data has already been logged, so my x-axis range is now [0,4] instead of [0,16]. Is there a way to square each element of "results" before calling hist? Regards Andrew [[alternative HTML version deleted]]

Andrew It seems that you want to call the default 'hist' function from the graphics package. You can do so by saying graphics::hist.default That function expects a vector, and one way of obtaining that is by 'exprs', so that altogether you could try graphics::hist.default( exprs(results), breaks=100, col="skyblue") Hope this helps, Wolfgang On 13/09/10 16:55, Andrew Einhorn wrote: > Hi there > > I would like to generate a histogramof my data after normalision using oligo > rma. See code below. > > library(oligo) > celfiles<- list.celfiles("cel_files",full.names = T) > twfs<- read.celfiles(celfiles) > results<- rma(twfs) > hist(results) > > The hist implementation in this instance takes the log2 of the expression > set elements before making the plot. This is a problem since the data has > already been logged, so my x-axis range is now [0,4] instead of [0,16]. > > Is there a way to square each element of "results" before calling hist? > > Regards > > Andrew > > [[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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber