That solved it. thought I had all the dependencies installed. Thanks. On Apr 24, 2007, at 11:00 AM, James W. MacDonald wrote: > Hi Erik, > > Erik Dopman wrote: >> I want to normalize for print order in limma, but I am running >> into trouble using the function when method='plate' because: >> Error in FUN(X[[1]], ...) : could not find function "huber" >> I am running R 2.4.1 and limma 2.9.17. Can someone supply me with >> the function "huber" so the normalization function works? Is >> there another work-around? > > Have you tried help.search()? I get this: > > > help.search("huber") > Help files with alias or concept or title matching 'huber' using fuzzy > matching: > > > > huber(MASS) Huber M-estimator of Location with MAD Scale > hubers(MASS) Huber Proposal 2 Robust Estimator of Location > and/or Scale > rlm(MASS) Robust Fitting of Linear Models > > So you may need a library(MASS) first. > > Best, > > Jim > > >> Cheers, >> Erik >> _______________________________________________ >> 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 > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and > should not be used for urgent or sensitive issues.

Dear List: I am running R v 2.4.1 and limma v 2.9.17, both of which were recently installed from older versions. Since making the update to newer versions, I am now unable to run my weight function in the read.maimages function. The error that I am receiving is: Warning message: the condition has length > 1 and only the first element will be used in: if (text.to.search != "") for (i in 1:ncn) { Has anybody run into this problem before? My overly redundant filter function and scan statement is below. Thanks, Erik filter <- function(x) { ifforeground <- ( (x[,"% > B635+2SD"] > 70 | x[,"% > B532+2SD"] > 70) & (x[,"F635 Median - B635"] > 4 * x[,"B635 SD"]) & (x[,"F532 Median - B532"] > 4 * x[,"B532 SD"]) & x[,"F635 % Sat."] < 30 & x[,"F532 % Sat."] < 30 & x[,"Dia."] > 60 & (x[,"B635 Mean"] < (1.2 * x[,"B635 Median"]) & x[,"B532 Mean"] < (1.2 * x[,"B532 Median"])) & (x[,"Ratio of Medians (635/532)"] < (1.2 * x[,"Rgn Ratio (635/532)"]) | x[,"Ratio of Medians (635/532)"] > (0.8 * x[,"Rgn Ratio (635/532)"])) & x[,"Sum of Medians (635/532)"] > 1000 ) ifnotflag <- x$Flags >= 0 return(as.numeric(ifnotflag & ifforeground)) } RG <- read.maimages(targets, source="genepix", columns=list(Rf="F635 Median", Gf="F532 Median", Rb="B635 Median", Gb="B532 Median"), other.columns=list("B635 SD", "B532 SD", "F635 Median - B635", "F532 Median - B532", "% > B635+2SD", "% > B532+2SD", "F635 % Sat.", "F532 % Sat.", "Dia.", "Ratio of Medians (635/532)", "Rgn Ratio (635/532)", "B635 Mean", "B635 Median", "B532 Mean", "B532 Median", "Median of Ratios (635/532)", "Sum of Medians (635/532)"), wt.fun = filter)