Hi, I want to make a qqplot for each CEL file in an affybatch. library(affy) library(hgu95av2cdf) library(hgu95av2probe) library(matchprobes) data(hgu95av2probe) summary(hgu95av2probe) getwd() setwd("C:/Program Files/R/rw2001/Normal") Data <- ReadAffy() length(Data) file.names<-c("01.CEL", "02.CEL", "03.CEL", "04.CEL", "05.CEL", "06.CEL","07.CEL", "08.CEL", "09.CEL", "10.CEL", "11.CEL", "12.CEL", "13.CEL", "14.CEL","15.CEL","16.CEL","17.CEL") M<-read.affybatch(filenames=file.names, description=NULL,notes="",compress=F, rm.mask=F,rm.outliers=F,rm.extra=F,verbose=T) But i get this error: > qqplot(M[,1]) Error in sort(x) : `x' must be atomic Thanks, Hrishi

Did you get my previous emails about ReadAffy, read.affybatch, setting column names from file names? Your 'Data' and 'M' should be the same ! Plotting operation do not need to necessarily have to work on AffyBatch objects. If you extract it using exprs() into a matrix, more options are possible. See help("AffyBatch") or example below : library(affy) data(affybatch.example) class(affybatch.example) [1] "AffyBatch" out <- rma(affybatch.example) e <- exprs(out) class(e) [1] "matrix" dim(e) [1] 10000 3 par(mfrow=c(1,3)) for(i in 1:3){ qqnorm( e[ ,i] ); qqline( e[ ,i] ) } Regards, Adai On Sat, 2005-03-19 at 08:02 -0800, Hrishikesh Deshmukh wrote: > Hi, > > I want to make a qqplot for each CEL file in an > affybatch. > library(affy) > library(hgu95av2cdf) > library(hgu95av2probe) > library(matchprobes) > data(hgu95av2probe) > summary(hgu95av2probe) > > getwd() > setwd("C:/Program Files/R/rw2001/Normal") > Data <- ReadAffy() > length(Data) > file.names<-c("01.CEL", "02.CEL", "03.CEL", > "04.CEL", "05.CEL", > "06.CEL","07.CEL", "08.CEL", "09.CEL", "10.CEL", > "11.CEL", "12.CEL", "13.CEL", > "14.CEL","15.CEL","16.CEL","17.CEL") > M<-read.affybatch(filenames=file.names, > description=NULL,notes="",compress=F, > > rm.mask=F,rm.outliers=F,rm.extra=F,verbose=T) > > But i get this error: > > qqplot(M[,1]) > Error in sort(x) : `x' must be atomic > > Thanks, > Hrishi > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi Adai, I did get your emails and right now i am going through the docs. I am interested in looking at actual signal intensities(with and without background correction) and then do like simple summary statistics like calculate mean/median/mode, look at how the signal distribution(s). Your sample helped a lot. Thanks, Hrishi --- Adaikalavan Ramasamy <ramasamy@cancer.org.uk> wrote: > Did you get my previous emails about ReadAffy, > read.affybatch, setting > column names from file names? Your 'Data' and 'M' > should be the same ! > > Plotting operation do not need to necessarily have > to work on AffyBatch > objects. If you extract it using exprs() into a > matrix, more options are > possible. See help("AffyBatch") or example below : > > library(affy) > data(affybatch.example) > class(affybatch.example) > [1] "AffyBatch" > > out <- rma(affybatch.example) > e <- exprs(out) > class(e) > [1] "matrix" > dim(e) > [1] 10000 3 > > par(mfrow=c(1,3)) > for(i in 1:3){ qqnorm( e[ ,i] ); qqline( e[ ,i] ) } > > Regards, Adai > > > > On Sat, 2005-03-19 at 08:02 -0800, Hrishikesh > Deshmukh wrote: > > Hi, > > > > I want to make a qqplot for each CEL file in an > > affybatch. > > library(affy) > > library(hgu95av2cdf) > > library(hgu95av2probe) > > library(matchprobes) > > data(hgu95av2probe) > > summary(hgu95av2probe) > > > > getwd() > > setwd("C:/Program Files/R/rw2001/Normal") > > Data <- ReadAffy() > > length(Data) > > file.names<-c("01.CEL", "02.CEL", "03.CEL", > > "04.CEL", "05.CEL", > > "06.CEL","07.CEL", "08.CEL", "09.CEL", > "10.CEL", > > "11.CEL", "12.CEL", "13.CEL", > > "14.CEL","15.CEL","16.CEL","17.CEL") > > M<-read.affybatch(filenames=file.names, > > > description=NULL,notes="",compress=F, > > > > rm.mask=F,rm.outliers=F,rm.extra=F,verbose=T) > > > > But i get this error: > > > qqplot(M[,1]) > > Error in sort(x) : `x' must be atomic > > > > Thanks, > > Hrishi > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >