affy: Trouble Creating Custom Processing Methods for summary expression
1
0
Entering edit mode
@alexander-c-cambon-1251
Last seen 9.6 years ago
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
rae230a rae230a • 1.1k views
ADD COMMENT
0
Entering edit mode
Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 9.6 years ago
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
ADD COMMENT

Login before adding your answer.

Traffic: 595 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6