[BioC] Still not working masking of features

[Laurent Gautier]

Dear Isaac, the error you report seems to be more in the function
ReadAffy than in 'readcelfile' (according to the dump you provide).
Generally, do not hesitate to send us the version number of your R
installation and the platform you use....

The following is the output from an R session performed on a Linux box (Mandrake 8.2)
a couple of minutes ago:

> tagada <- list()
> tagada[1] <- "/mnt/cdrom/LatinSquare/E_coli/000825_bgd_Ds11.CEL.gz"
> tagada[2] <- "/mnt/cdrom/LatinSquare/E_coli/000825_bgd_Ds10.CEL.gz"
> mynames <- c("a", "b")
> p <- ReadAffy("/mnt/cdrom/LatinSquare/E_coli/1286_S01.CDF.gz", tagada, compress.cel=T, compress.cdf=T, chip.names=mynames, rm.mask=T)
reading CDF file
processing information
reading 2 CEL files..
preparing probe level object
> p
Plob object
CDF used=/mnt/cdrom/LatinSquare/E_coli/1286_S01.CDF.gz
number of chips=2
number of genes=9842
number of probe pairs=145443
annotation=
description=
notes=
size of chip=544x544
chip names=
a
b


>




We will look at it as soon as possible.

Are the fact that all probes get 'masked' and the error in ReadAffy
two different problems ? 
 



Regards,



Laurent

On Wed, Jun 19, 2002 at 04:26:21PM -0400, Isaac Neuhaus wrote:
> The funtion read.celfile is still giving me grief in version 1.1.1 this
> is what I get. (Just a as a remainder some probe sets have all of their
> features masked).
> 
> > cels<-list()
> > cels[1]<-"cw20001050101a.cel"
> > cels[2]<-"cw20001050102a.cel"
> > cels[3]<-"cw20001050103a.cel"
> > cels[4]<-"cw20001050104a.cel"
> > cels[5]<-"cw20001050105a.cel"
> > cels[6]<-"cw20001050106a.cel"
> > names<-list()
> > names[1]<-"CW20001050101A"
> > names[2]<-"CW20001050102A"
> > names[3]<-"CW20001050103A"
> > names[4]<-"CW20001050104A"
> > names[5]<-"CW20001050105A"
> > names[6]<-"CW20001050106A"
> > data <- ReadAffy(CDFfile="HG_U95Av2.CDF", CELfiles=cels,
> chip.names=names, rm.mask=T, verbose=F)
> Error in read.celfile(CELfiles[i], compress = compress.cel, sd = FALSE,
> :
>         subscript out of bounds
> Execution halted
> 
> Isaac
> 
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-- 
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Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent