[BioC] General question about library files

[Henrik Bengtsson]

Hi,

On Fri, Aug 15, 2008 at 1:12 PM, John O. Woods <bamboowarrior at gmail.com> wrote:
> Hi everyone,
>
> This is more of a general question. I'm fairly new to array analysis
> (jumping right into the deep end here, looking at whole-genome tiling
> arrays), and I'm having trouble sorting out in my head exactly what
> data is stored in each Affy filetype.

The document 'Affymetrix Data File Formats' by Affymetrix may be
useful (though technical but it does not leave anything behind):

http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/

/Henrik

>
> It seems obvious that the CEL files contain the raw intensities from
> the arrays themselves. Still, I'm not sure how these CELs are
> organized--is it one CEL per chip? How do I know which metadata files
> match with a specific CEL?
>
> I also see that the BPMAP files contain design information for the
> arrays. What I'm less clear on is why these have genome builds in the
> names. For example, I got NCBIv36 bpmaps from Harvard, but Affy makes
> an earlier build available (v34, I think). The probes are, of course,
> the same (right?). Thus, does it matter to Bioconductor which build
> I'm using?
>
> I'm much less clear on CIFs and CDFs. How do these differ, and what
> information do they contain? Affymetrix provides only very vague
> descriptions on its website: "The CDF file describes the layout for an
> Affymetrix GeneChip array." Gee, thanks. How does that differ from a
> BPMAP? Why do the makePdInfoBuilder code samples use CIFs instead of
> CDFs?
>
> I've been looking for a good resource to help me get a handle on this
> stuff. I see lots of tutorials and stuff for analyzing microarrays,
> but little for tiling arrays (yay cutting edge). Anyone have any
> pointers?
>
> Thanks so much for the help.
>
> Cheers,
> John Woods
>
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