[Bioc-sig-seq] (no subject) Changed: Overall directions

[Stephen Henderson]

I see. We are just in the process of buying a Solexa and people will be
using it for MeDIP-seq (methylation), and ChIP-seq (Trans Factors).


Stephen Henderson
Cancer Institute, Paul O'Gorman Building
Huntley Street, University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827
 
-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: 29 February 2008 17:24
To: Stephen Henderson
Cc: bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] (no subject) Changed: Overall directions

"Stephen Henderson" <s.henderson at ucl.ac.uk> writes:

> OK
>
> Perhaps I can be first by asking what tasks you plan to cover? And how
> do you plan to implement them in R (given the memory restrictions)? Do
> you plan a nice front end for lots of C-code?

Hi Stephen --

It'll depend of course on who in the community steps up. Probably
packages will start as a standard R interface that gets the job done,
with pretty gui's later. Probably an early step (though perhaps not
the very first) will be settling on a common set of S4-style classes
to represent experiments and data, in the manner of an ExpressionSet.

>From our end, our first pass is to assume that computer resources are
not really an issue -- a 2 or 4 GB 32-bit operating system is not what
we're targeting.

Also in terms of preliminary experience, it seems like some operations
can be done effectively at the R level (data input and QA assessment)
but that some important steps (e.g., alignments) require clever data
structures and algorithms that get implemented in C. It's also
possible for some questions to exploit the structure of the data,
e.g., analyzing Solexa data in manageable chunks corresponding to
individual tiles.

Martin

> Stephen Henderson
>
> Cancer Institute, Paul O'Gorman Building
>
> Gower Street, University College London
>
> United Kingdom, WC1E 6BT
>
> +44 (0)207 679 6827
>
>  
>
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

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