Hello,
I want to read .DAT files using Bioconductor. Is it
possible to do so or do I need to get the .CEL files
to perform the analysis. Please guide me.
Thanking you,
Tapan Mehta
On Tue, Feb 11, 2003 at 12:31:18PM -0800, Tapan Mehta wrote:
> Hello,
>
> I want to read .DAT files using Bioconductor. Is it
> possible to do so or do I need to get the .CEL files
> to perform the analysis. Please guide me.
>
> Thanking you,
>
> Tapan Mehta
>
As far as I could figure it out, .DAT is a sort of Affymetrix
tweaked tiff format (chip scan + grid). MAS (and may be 'dchip')
only can deal with them. Unless somebody speaks
up to suggests otherwise, you'll have to get the CEL from
the DAT oustide bioconductor...
Hopin' it helps,
L.
AFAIK the Affymetrix DAT format is actually very simple (though its
been quite some time since I looked at a DAT file). It is just a block
of 16-bit intensity values in a simple raw format after a 512-byte
header. The header contains the gridding information and well as the
image extents... If you have photoshop around, you can actually open
the DAT file in Photoshop using the "RAW" file format if you like :-)
On Tuesday, February 11, 2003, at 10:12 PM, Laurent Gautier wrote:
> On Tue, Feb 11, 2003 at 12:31:18PM -0800, Tapan Mehta wrote:
>> Hello,
>>
>> I want to read .DAT files using Bioconductor. Is it
>> possible to do so or do I need to get the .CEL files
>> to perform the analysis. Please guide me.
>>
>> Thanking you,
>>
>> Tapan Mehta
>>
>
> As far as I could figure it out, .DAT is a sort of Affymetrix
> tweaked tiff format (chip scan + grid). MAS (and may be 'dchip')
> only can deal with them. Unless somebody speaks
> up to suggests otherwise, you'll have to get the CEL from
> the DAT oustide bioconductor...
>
>
> Hopin' it helps,
>
> L.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
Byron Ellis (bellis@hsph.harvard.edu)
"Oook" - The Librarian
Hello,
Thank you for the help. I will try this method.
Tapan Mehta
--- Byron Ellis <bellis@hsph.harvard.edu> wrote:
> AFAIK the Affymetrix DAT format is actually very
> simple (though its
> been quite some time since I looked at a DAT file).
> It is just a block
> of 16-bit intensity values in a simple raw format
> after a 512-byte
> header. The header contains the gridding information
> and well as the
> image extents... If you have photoshop around, you
> can actually open
> the DAT file in Photoshop using the "RAW" file
> format if you like :-)
>
> On Tuesday, February 11, 2003, at 10:12 PM, Laurent
> Gautier wrote:
>
> > On Tue, Feb 11, 2003 at 12:31:18PM -0800, Tapan
> Mehta wrote:
> >> Hello,
> >>
> >> I want to read .DAT files using Bioconductor. Is
> it
> >> possible to do so or do I need to get the .CEL
> files
> >> to perform the analysis. Please guide me.
> >>
> >> Thanking you,
> >>
> >> Tapan Mehta
> >>
> >
> > As far as I could figure it out, .DAT is a sort of
> Affymetrix
> > tweaked tiff format (chip scan + grid). MAS (and
> may be 'dchip')
> > only can deal with them. Unless somebody speaks
> > up to suggests otherwise, you'll have to get the
> CEL from
> > the DAT oustide bioconductor...
> >
> >
> > Hopin' it helps,
> >
> > L.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> >
>
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
> Byron Ellis (bellis@hsph.harvard.edu)
> "Oook" - The Librarian
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
>
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
you got many useful answers about the DAT files. to answer your
question
about the CELs.. for now you need them if you want to use the affy
package. the MAS software will do that.
there are some that have alternate
ways of going from DAT to CEL. harry zuzan and davit cutler (cc-ed)
are
two that come to mind.
-rafael
On Tue, 11 Feb 2003, Tapan Mehta wrote:
> Hello,
>
> I want to read .DAT files using Bioconductor. Is it
> possible to do so or do I need to get the .CEL files
> to perform the analysis. Please guide me.
>
> Thanking you,
>
> Tapan Mehta
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
On Linux, I've been using the rawtopgm utility followed by the convert
utility to obtain a file that can be viewed.
> Date: Tue, 11 Feb 2003 22:37:20 -0500
> Subject: Re: [BioC] Reading of .DAT files using Bioconductor
> Cc: bioconductor@stat.math.ethz.ch, Tapan Mehta <tapmehta@yahoo.com>
> To: Laurent Gautier <laurent@cbs.dtu.dk>
> From: Byron Ellis <bellis@hsph.harvard.edu>
>
> AFAIK the Affymetrix DAT format is actually very simple (though its
> been quite some time since I looked at a DAT file). It is just a
block
> of 16-bit intensity values in a simple raw format after a 512-byte
> header. The header contains the gridding information and well as the
> image extents... If you have photoshop around, you can actually open
> the DAT file in Photoshop using the "RAW" file format if you like
:-)
