[BioC] qqplot

[Hrishikesh Deshmukh]

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 at 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
> > 
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
>