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

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 -- Ben Bolstad <bolstad at="" stat.berkeley.edu=""> http://www.stat.berkeley.edu/~bolstad