[BioC] qqplot

[Adaikalavan Ramasamy]

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
> 
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