Thanks for your help, Ben. The changes you made below work for my data set too. It also helps considerably to load the MASS pacakge ( since I had forgotten to put in the code for the huber function that you had in your vignette). Alex >>> Ben Bolstad <bolstad at="" stat.berkeley.edu=""> 06/10/05 11:20 PM >>> This is my code: library(affy);library(affydata); library(MASS) data(Dilution) # demonstration data generateExprVal.method.huber <- function(probes) { res <- apply(probes, 2, huber) mu <- unlist(lapply(res, function(x) x$mu)) s <- unlist(lapply(res, function(x) x$s)) return(list(exprs = mu, se.exprs = s)) } ###generateExprSet.methods <- c(generateExprSet.methods, "huber") express.summary.stat.methods<-c(express.summary.stat.methods,"huber") eset.bg.huber<-expresso(Dilution, bgcorrect.method="mas", pmcorrect.method="pmonly", summary.method="huber") exprs(eset.bg.huber)[1:10,] My results: > exprs(eset.bg.huber)[1:10,] 20A 20B 10A 10B 1000_at 435.75360 402.08952 411.59458 362.68261 1001_at 91.53807 85.69595 84.98978 77.48265 1002_f_at 176.19728 162.36399 146.33448 152.49209 1003_s_at 238.53642 193.41824 205.91676 209.08518 1004_at 176.02760 159.17141 164.96742 155.93032 1005_at 502.82416 526.42168 452.69040 465.98990 1006_at 76.96024 69.57741 73.88633 63.37821 1007_s_at 605.03563 591.35033 537.21003 546.18388 1008_f_at 545.60434 513.74078 616.34378 574.13054 1009_at 1959.30326 1986.06121 2118.56979 2007.63819 > > >>> Ben Bolstad <bolstad at="" stat.berkeley.edu=""> 06/10/05 6:30 PM >>> > Try renaming "computeExprVal.huber" to "generateExprVal.method.huber". > That should make it work. I think summary methods for expresso need to > have the "generateExprVal.method." prefix. I will fix the vignette > accordingly. > > Ben > > > > > > > On Fri, 2005-06-10 at 16:52 -0400, Alexander C Cambon wrote: > > I am trying to use the "Custom Processing Methods" available in package "affy" to create new expression methods. But for some reason I am getting "NA"'s for the expression values. I start out using 4 cel files with rae230a data. > > > > > x > > AffyBatch object > > size of arrays=602x602 features (11330 kb) > > cdf=RAE230A (15923 affyids) > > number of samples=4 > > number of genes=15923 > > annotation=rae230a > > > > ## And I proceed by using the example in the "Custom Processing Methods (How To)" vignette on page 4: > > > > > computeExprVal.huber <- function(probes) { > > + res <- apply(probes, 2, huber) > > + mu <- unlist(lapply(res, function(x) x$mu)) > > + s <- unlist(lapply(res, function(x) x$s)) > > + return(list(exprs = mu, se.exprs = s)) > > + } > > > > >generateExprSet.methods <- c(generateExprSet.methods, "huber") > > > > ###Then I use the expresso function... and get an error message (see below) > > > > >eset.bg.huber<-expresso(x, bgcorrect.method="mas", pmcorrect.method="pmonly", > > + summary.method="huber") > > background correction: mas > > PM/MM correction : pmonly > > expression values: huber > > background correcting...done. > > normalizing...done. > > Error in match.arg(summary.method, express.summary.stat.methods) : > > 'arg' should be one of avgdiff, liwong, mas, medianpolish, playerout > > > > ## So, after looking at the error, I decide to add (perhaps wrongly) the line > > > > > express.summary.stat.methods<-c(express.summary.stat.methods,"huber") > > > > ## and I rerun... > > > > >eset.bg.trm<-expresso(x, bgcorrect.method="mas", pmcorrect.method="pmonly", > > + summary.method="huber") > > > > > > ## Now I get: > > > > background correction: mas > > normalization: > > PM/MM correction : pmonly > > expression values: huber > > background correcting...done. > > normalizing...done. > > 15923 ids to be processed > > | | > > |####################| > > > > ## This looks reassuring, and I start thinking I am over the hump. However when I ask for the first few lines, I get all ##"NA"'s for expression .. > > > > > exprs(eset.bg.huber)[1:10,1:4] > > AK_0A.CEL AK_0B.CEL AK_4A.CEL AK_4B.CEL > > 1367452_at NA NA NA NA > > 1367453_at NA NA NA NA > > 1367454_at NA NA NA NA > > 1367455_at NA NA NA NA > > 1367456_at NA NA NA NA > > 1367457_at NA NA NA NA > > 1367458_at NA NA NA NA > > 1367459_at NA NA NA NA > > > > ###But when I do the same thing, using a "built-in" expresso method (using "x"), I get > > > > > exprs(eset44)[1:10,1:4] > > AK_0A.CEL AK_0B.CEL AK_4A.CEL AK_4B.CEL > > 1367452_at 564.68667 400.93697 476.22935 396.00641 > > 1367453_at 330.41054 281.98687 279.02867 305.24909 > > 1367454_at 158.99028 165.78677 134.08273 151.77046 > > 1367455_at 302.39252 223.56433 192.13621 204.74223 > > 1367456_at 881.07080 931.81819 792.18972 583.09672 > > 1367457_at 139.75233 142.67949 140.01944 153.02465 > > 1367458_at 144.34063 154.16194 176.33189 190.89218 > > 1367459_at 1010.72613 709.47988 886.92512 957.64834 > > 1367460_at 48.19831 51.70533 59.43114 54.13907 > > 1367461_at 213.03203 194.16510 210.99492 182.22481 > > > > Any ideas what I am doing wrong? > > > > Alex > > > > > > > > Alexander Cambon > > Biostatistician > > School of Public Health > > Dept of Biostatistics and Bioinformatics > > University of Louisville > > > > R 2.1.0 > > Bioconductor 1.6 > > Windows XP > > Dell Optiplex > > 1 GB RAM > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor