problems rma() with mouse exon affy data in exonmap package
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bruce ▴ 20
@bruce-2349
Last seen 9.6 years ago
Dear all: I currently faced this error when I tried the rma() with two sample of mouse exon affy data. I appreciate get help from you! Below is the whole process: /*********************************************************** covdesc file's: treatment Xu_1.CEL a Xu_2.CEL b >library(exonmap) >rawdata<-read.exon() >rawdata at cdfName<-"mouseexonpmcdf" > rawdata.rma<-rma(rawdata) Background correcting Error in density.default(x, kernel = "epanechnikov", n = 2^14) : 'x' contains missing values > ls() [1] "rawdata" > sessionInfo() R version 2.5.0 (2007-04-23) i686-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF8;LC_NUMERIC=C;LC_TIME=en_US.UTF8; LC_COLLATE=en_US.UTF8;LC_MONETARY=en_US.UTF8; LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" [7] "utils" "methods" "base" other attached packages: mouseexonpmcdf exonmap plier RMySQL DBI "1.1" "1.0.06" "1.6.0" "0.6-0" "0.2-3" RColorBrewer simpleaffy genefilter survival affy "1.0-1" "2.10.31" "1.14.1" "2.31" "1.14.2" affyio Biobase "1.4.1" "1.14.1" > thanks bruce -- Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences Email:chen_zhaoming at gibh.ac.cn,neamee at gmail.com http://www.gibh.ac.cn Office:020-32290510 Mobile:13480217655
Survival cdf genefilter affy simpleaffy plier exonmap Survival cdf genefilter affy • 1.3k views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States
Hi Bruce, bruce wrote: > Dear all: > > I currently faced this error when I tried the rma() with two sample > of mouse exon affy data. > > I appreciate get help from you! > > Below is the whole process: > > /*********************************************************** > > covdesc file's: > > treatment > > Xu_1.CEL a > > Xu_2.CEL b > > >> library(exonmap) > >> rawdata<-read.exon() > >> rawdata at cdfName<-"mouseexonpmcdf" What do you get if you type rawdata at an R prompt? How about sumis.na(pm(rawdata))) ? Best, Jim > >> rawdata.rma<-rma(rawdata) > > Background correcting > > Error in density.default(x, kernel = "epanechnikov", n = 2^14) : > > 'x' contains missing values > >> ls() > > [1] "rawdata" > >> sessionInfo() > > R version 2.5.0 (2007-04-23) > > i686-redhat-linux-gnu > > > locale: > > LC_CTYPE=en_US.UTF8;LC_NUMERIC=C;LC_TIME=en_US.UTF8; > > LC_COLLATE=en_US.UTF8;LC_MONETARY=en_US.UTF8; > > LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; > > LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; > > LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > > attached base packages: > > [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" > > [7] "utils" "methods" "base" > > > other attached packages: > > mouseexonpmcdf exonmap plier RMySQL DBI > > "1.1" "1.0.06" "1.6.0" "0.6-0" "0.2-3" > > RColorBrewer simpleaffy genefilter survival affy > > "1.0-1" "2.10.31" "1.14.1" "2.31" "1.14.2" > > affyio Biobase > > "1.4.1" "1.14.1" > > thanks > bruce -- 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
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Can you really use rma with just 2 arrays? --Naomi At 08:22 AM 8/29/2007, James W. MacDonald wrote: >Hi Bruce, > >bruce wrote: > > Dear all: > > > > I currently faced this error when I tried the rma() with two sample > > of mouse exon affy data. > > > > I appreciate get help from you! > > > > Below is the whole process: > > > > /*********************************************************** > > > > covdesc file's: > > > > treatment > > > > Xu_1.CEL a > > > > Xu_2.CEL b > > > > > >> library(exonmap) > > > >> rawdata<-read.exon() > > > >> rawdata at cdfName<-"mouseexonpmcdf" > >What do you get if you type > >rawdata > >at an R prompt? > >How about > >sumis.na(pm(rawdata))) > >? > >Best, > >Jim > > > > > >> rawdata.rma<-rma(rawdata) > > > > Background correcting > > > > Error in density.default(x, kernel = "epanechnikov", n = 2^14) : > > > > 'x' contains missing values > > > >> ls() > > > > [1] "rawdata" > > > >> sessionInfo() > > > > R version 2.5.0 (2007-04-23) > > > > i686-redhat-linux-gnu > > > > > > locale: > > > > LC_CTYPE=en_US.UTF8;LC_NUMERIC=C;LC_TIME=en_US.UTF8; > > > > LC_COLLATE=en_US.UTF8;LC_MONETARY=en_US.UTF8; > > > > LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; > > > > LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; > > > > LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > > > > > attached base packages: > > > > [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" > > > > [7] "utils" "methods" "base" > > > > > > other attached packages: > > > > mouseexonpmcdf exonmap plier RMySQL DBI > > > > "1.1" "1.0.06" "1.6.0" "0.6-0" "0.2-3" > > > > RColorBrewer simpleaffy genefilter survival affy > > > > "1.0-1" "2.10.31" "1.14.1" "2.31" "1.14.2" > > > > affyio Biobase > > > > "1.4.1" "1.14.1" > > > > thanks > > bruce > >-- >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 > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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You can debate the wisdom or otherwise of using only a small number of arrays on a philosophical or technical metric basis all you want. But the error mentioned below is unrelated to the number of arrays used. In fact the rma() function will happily process two or even a single array without complaint. What Jim is alluding to with his question is that rma() does not expect to be fed NA PM probe intensities. Best, Ben On Wed, 2007-08-29 at 10:00 -0400, Naomi Altman wrote: > Can you really use rma with just 2 arrays? > > --Naomi > > At 08:22 AM 8/29/2007, James W. MacDonald wrote: > >Hi Bruce, > > > >bruce wrote: > > > Dear all: > > > > > > I currently faced this error when I tried the rma() with two sample > > > of mouse exon affy data. > > > > > > I appreciate get help from you! > > > > > > Below is the whole process: > > > > > > /*********************************************************** > > > > > > covdesc file's: > > > > > > treatment > > > > > > Xu_1.CEL a > > > > > > Xu_2.CEL b > > > > > > > > >> library(exonmap) > > > > > >> rawdata<-read.exon() > > > > > >> rawdata at cdfName<-"mouseexonpmcdf" > > > >What do you get if you type > > > >rawdata > > > >at an R prompt? > > > >How about > > > >sumis.na(pm(rawdata))) > > > >? > > > >Best, > > > >Jim > > > > > > > > > >> rawdata.rma<-rma(rawdata) > > > > > > Background correcting > > > > > > Error in density.default(x, kernel = "epanechnikov", n = 2^14) : > > > > > > 'x' contains missing values > > > > > >> ls() > > > > > > [1] "rawdata" > > > > > >> sessionInfo() > > > > > > R version 2.5.0 (2007-04-23) > > > > > > i686-redhat-linux-gnu > > > > > > > > > locale: > > > > > > LC_CTYPE=en_US.UTF8;LC_NUMERIC=C;LC_TIME=en_US.UTF8; > > > > > > LC_COLLATE=en_US.UTF8;LC_MONETARY=en_US.UTF8; > > > > > > LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; > > > > > > LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; > > > > > > LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > > > > > > > > attached base packages: > > > > > > [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" > > > > > > [7] "utils" "methods" "base" > > > > > > > > > other attached packages: > > > > > > mouseexonpmcdf exonmap plier RMySQL DBI > > > > > > "1.1" "1.0.06" "1.6.0" "0.6-0" "0.2-3" > > > > > > RColorBrewer simpleaffy genefilter survival affy > > > > > > "1.0-1" "2.10.31" "1.14.1" "2.31" "1.14.2" > > > > > > affyio Biobase > > > > > > "1.4.1" "1.14.1" > > > > > > thanks > > > bruce > > > >-- > >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 > > > >_______________________________________________ > >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 > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > 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
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Hi Jim,Ben and Naomi: Thanks for your help. The rawdata and sum of it's missing value information follows below: > rawdata AffyBatch object size of arrays=2560x2560 features (8 kb) cdf=mouseexonpmcdf (1201338 affyids) number of samples=2 number of genes=1201338 annotation=moex10stv1 notes= > sumis.na(pm(rawdata))) [1] 17940 > summary(exprs(rawdata)) Xu_1.CEL Xu_2.CEL Min. : 19.0 Min. : 19.0 1st Qu.: 33.0 1st Qu.: 34.0 Median : 50.0 Median : 57.0 Mean : 263.7 Mean : 287.5 3rd Qu.: 114.0 3rd Qu.: 140.0 Max. :23585.0 Max. :23777.0 NA's :26215.0 Sincerely Bruce On Wed, 2007-08-29 at 07:40 -0700, Ben Bolstad wrote: > You can debate the wisdom or otherwise of using only a small number of > arrays on a philosophical or technical metric basis all you want. But > the error mentioned below is unrelated to the number of arrays used. In > fact the rma() function will happily process two or even a single array > without complaint. What Jim is alluding to with his question is that > rma() does not expect to be fed NA PM probe intensities. > > Best, > > Ben > > > On Wed, 2007-08-29 at 10:00 -0400, Naomi Altman wrote: > > Can you really use rma with just 2 arrays? > > > > --Naomi > > > > At 08:22 AM 8/29/2007, James W. MacDonald wrote: > > >Hi Bruce, > > > > > >bruce wrote: > > > > Dear all: > > > > > > > > I currently faced this error when I tried the rma() with two sample > > > > of mouse exon affy data. > > > > > > > > I appreciate get help from you! > > > > > > > > Below is the whole process: > > > > > > > > /*********************************************************** > > > > > > > > covdesc file's: > > > > > > > > treatment > > > > > > > > Xu_1.CEL a > > > > > > > > Xu_2.CEL b > > > > > > > > > > > >> library(exonmap) > > > > > > > >> rawdata<-read.exon() > > > > > > > >> rawdata at cdfName<-"mouseexonpmcdf" > > > > > >What do you get if you type > > > > > >rawdata > > > > > >at an R prompt? > > > > > >How about > > > > > >sumis.na(pm(rawdata))) > > > > > >? > > > > > >Best, > > > > > >Jim > > > > > > > > > > > > > >> rawdata.rma<-rma(rawdata) > > > > > > > > Background correcting > > > > > > > > Error in density.default(x, kernel = "epanechnikov", n = 2^14) : > > > > > > > > 'x' contains missing values > > > > > > > >> ls() > > > > > > > > [1] "rawdata" > > > > > > > >> sessionInfo() > > > > > > > > R version 2.5.0 (2007-04-23) > > > > > > > > i686-redhat-linux-gnu > > > > > > > > > > > > locale: > > > > > > > > LC_CTYPE=en_US.UTF8;LC_NUMERIC=C;LC_TIME=en_US.UTF8; > > > > > > > > LC_COLLATE=en_US.UTF8;LC_MONETARY=en_US.UTF8; > > > > > > > > LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; > > > > > > > > LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; > > > > > > > > LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > > > > > > > > > > > attached base packages: > > > > > > > > [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" > > > > > > > > [7] "utils" "methods" "base" > > > > > > > > > > > > other attached packages: > > > > > > > > mouseexonpmcdf exonmap plier RMySQL DBI > > > > > > > > "1.1" "1.0.06" "1.6.0" "0.6-0" "0.2-3" > > > > > > > > RColorBrewer simpleaffy genefilter survival affy > > > > > > > > "1.0-1" "2.10.31" "1.14.1" "2.31" "1.14.2" > > > > > > > > affyio Biobase > > > > > > > > "1.4.1" "1.14.1" > > > > > > > > thanks > > > > bruce > > > > > >-- > > >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 > > > > > >_______________________________________________ > > >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 > > > > Naomi S. Altman 814-865-3791 (voice) > > Associate Professor > > Dept. of Statistics 814-863-7114 (fax) > > Penn State University 814-865-1348 (Statistics) > > University Park, PA 16802-2111 > > > > _______________________________________________ > > 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 > > -- Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences ?????????????????????????????????? http://www.gibh.ac.cn Email:chen_zhaoming at gibh.ac.cn,neamee at gmail.com Office:020-32290510 Mobile:13480217655
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