[BioC] DAT files

[James W. MacDonald]

Hi Alex,

On 6/9/2011 6:37 AM, Aleksandra .. wrote:
> Hi everyone!
>
> I am quite new to Bioconductor project. Is there a possibility to read and
> manipulate DAT files that come from Affymetrix? I tried to read it as simple
> .dat file, but instead of reading the image R brings this line to me:
>
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>    scan() expected 'a real', got '�}}'
>
> I guess this is not a normal DAT file, so if anybody has any

That _is_ a normal DAT file. They have been binary format for years now, 
so you will not be able to read in as if they are simple text files.

> information on how can I play with affymetrix dat files, let me know.

I don't think there are packages that are designed explicitly to work 
directly with DAT files. In addition, you would have to get the file 
that Affymetrix uses to grid the individual pixels into probe regions, 
and I have never seen that file used outside of Affy's own products.

The first place to look would be the Affymetrix SDK to see if they even 
expose functions for working with DAT files. Then you could either 
modify the affxparser package to use those functions (if they exist), or 
plead mightily with Kaspar, Henrik or James to see if they would add them.

Best,

Jim


>
> Thank you in advance!
>
> Alex
>
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>
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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