Thanks for your replies. I've managed to solve the problem although im still
not sure why the other files were corrupt. The data Henrik has referred to
is indeed the data that I extracted from the Affymetrix webstie - the
chromsome X data in the form of DTT files. Initially I used the Affymetrix
Data Transfer Tool to extract the CEL files on a windows based machine. I
then transferred these CEL files over to my main linux machine, however
somewhere during the transfer process they became corrupt. I can say this
because I am able to successfully read in the CEL files in R on my windows
machine and I get exactly the same file information as Hendrik has shown.

So instead of transferring the files, I followed Hendrik's tutorial on
extracting the CEL files from the DTT files in UNIX and it has worked to
perfection! Thanks so much for your help. That was very useful.

Best regards,
Matt

On Tue, May 13, 2008 at 5:53 PM, Henrik Bengtsson <hb@stat.berkeley.edu>
wrote:

> Hi,
>
> On Tue, May 13, 2008 at 12:31 PM, Robert Gentleman <rgentlem@fhcrc.org>
> wrote:
> > Hi Matt,
> >
> >
> >  Matt K wrote:
> >
> > > I am having problems reading in some publicly available chromosome X
> > > titration Nsp chip CEL files. The data are available from the
> Affymetrix
> > > website:
> > >
> > >
> >
> http://www.affymetrix.com/support/technical/sample_data/copy_number_data.affx
> > >
> >
> >   I did not see any file there that obviously contained the CEL files,
> can
> > you say what you downloaded (provided the questions below don't solve
> your
> > problem).
>
> FYI/for the record, they are in the *.DTT files (basically a *.zip
> archive split in many files).  It is quite tedious to extract the
> files if you don't have the right tools, but it is still possible with
> a basic Unix setup.  See
>
> http://groups.google.com/group/aroma-affymetrix/web/mapping250k-nsp-mapping250k-sty
> and the reference to Page 'Affymetrix multi-part DTT/ZIP archives' for
> the details.
>
> >
> >
> >
> > >
> > > I have not modified the data in anyway. Here is what happens when I try
> to
> > > read the data:
> > >
> > >
> > > > library(affxparser)
> > > > path <- "./rawData/3X/Mapping250K_Nsp/"
> > > > pathnames <- list.files(path=path, pattern="[.](cel|CEL)$",
> > > >
> > > full.names=TRUE)
> > >
> > > > pathnames
> > > >
> > > [1] "./rawData/3X/Mapping250K_Nsp//NA04626_NSP_R1.CEL"
> > > [2] "./rawData/3X/Mapping250K_Nsp//NA04626_NSP_R2.CEL"
> > > [3] "./rawData/3X/Mapping250K_Nsp//NA04626_NSP_R3.CEL"
> > > [4] "./rawData/3X/Mapping250K_Nsp//NA04626_NSP_R4.CEL"
> > >
> > > > hdr <- readCelHeader(pathnames[1])
> > > >
> > > terminate called after throwing an instance of
> > > 'affymetrix_calvin_exceptions::UnableToOpenFileException'
>
> That is sometime how 'affxparser' responds to corrupt files.  There is
> currently no exception handling at the native-code level in affxparser
> causing it to core dump on bad files.  It's on the to do list but with
> low priority.
>
> FYI, I've got those files as well and I can read the perfectly well
> using affxparser v1.11.3:
>
> library(affxparser);
> path <- "rawData/Affymetrix_2006-Chromosome_X/Mapping250K_Nsp/";
> pathnames <- list.files(pattern="[.]CEL$", path=path, full.names=TRUE);
> hdrs <- lapply(pathnames, readCelHeader);
>
> Since it is quite tricky that to extract the CEL files from the DTT
> files, you might have got something wrong there.  You might also have
> downloaded the DTT, D02, D03, ... files in text mode and not binary
> mode (adding/removing extract bytes).  My notes on
>
> http://groups.google.com/group/aroma-affymetrix/web/affymetrix-multi-part-dtt-zip-archives
> might shine some light on your problem.
>
> For your troubleshooting, here is are some details (make sure to have
> the latest version of 'digest' installed):
>
> library(digest);
> x <- lapply(pathnames, FUN=function(pathname) {
>  c(basename(pathname), file.info(pathname)$size, digest(file=pathname))
> });
> x <- as.data.frame(matrix(unlist(x), ncol=3, byrow=TRUE));
> colnames(x) <- c("filename", "bytes", "md5");
> print(x);
>
>             filename    bytes                              md5
> 1  NA01416_NSP_R1.CEL 65743954 edce95d22481a133bcadb4faa79eb8d5
> 2  NA01416_NSP_R2.CEL 65701910 89291d7fb32b43ce6a9c83716d3db747
> 3  NA01416_NSP_R3.CEL 65727988 fba34620e18b6b3de8ff3a394ed0e313
> 4  NA01416_NSP_R4.CEL 65730078 0b26c2ac467fda36182855eca1e005e5
> 5  NA04626_NSP_R1.CEL 65693986 e720285a271506ea79bcc067feb90066
> 6  NA04626_NSP_R2.CEL 65725339 e7934222ecd4b0f9f46bcea27aa53549
> 7  NA04626_NSP_R3.CEL 65703014 7300b841c8b7eafdd73f6272de7e551d
> 8  NA04626_NSP_R4.CEL 65712493 64a9c11f8bc268ea17632f23264f0be1
> 9  NA06061_NSP_R1.CEL 65741243 51cae8fcdf3761ef4ce5d68ef980dfce
> 10 NA06061_NSP_R2.CEL 65703467 01a19363f226765b5c3b10cd5607dc98
> 11 NA06061_NSP_R3.CEL 65721991 9fdc58f8036457caa3551bc9eb8cd046
> 12 NA06061_NSP_R4.CEL 65712766 e7fa2d9adf599fd29b80c121b7e4dfe7
>
> Hope this helps
>
> Henrik
>
> > >
> >
> >   That suggests that you may not have read permission on them. Did you
> check
> > and see if you could open those files with any other tool/editor?
> >
> >   You could just try and open them and read them using standard R tools
> to
> > see if that works (if they are binary CEL files then you will just get
> junk
> > from readLines, but that isn't the issue, you just want to know if they
> can
> > be opened from R).
> >
> >   Your R is out of date, and this sessionInfo is not correct, as you
> should
> > have had affxparser attached and it is not.  Please don't do that, mixing
> > and matching error messages and sessionInfo output makes life hard for
> > anyone that wants to help.  Step one is to update R and BioC...
> >
> >
> >
> >
> > >
> > > Process R aborted at Tue May 13 15:01:55 2008
> > >
> > > As you see R aborts. The same failure happens when I try to load in any
> of
> > > the other CEL files. My R session info is:
> > >
> > >
> > > > sessionInfo()
> > > >
> > > R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
> > > x86_64-unknown-linux-gnu
> > >
> > > locale:
> > >
> >
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;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] stats     graphics  grDevices utils     datasets  methods   base
> > >
> > > Thanks for any help.
> > >
> > > Matt
> > >
> > >        [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
> > >
> >
> >  --
> >  Robert Gentleman, PhD
> >  Program in Computational Biology
> >  Division of Public Health Sciences
> >  Fred Hutchinson Cancer Research Center
> >  1100 Fairview Ave. N, M2-B876
> >  PO Box 19024
> >  Seattle, Washington 98109-1024
> >  206-667-7700
> >  rgentlem@fhcrc.org
> >
> >
> >
> >  _______________________________________________
> >  Bioconductor mailing list
> >  Bioconductor@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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