You're right, there is no cel file management and that's one of many
warts needing fixing - it's not a lot of work to make a new tool to
create an eSet from a tarball of cel files as you suggest.
Unfortunately the rexpression toolkit will soon be deprecated and
disappear from the default distribution.
It's no longer under active development by me - the group I now work
with don't do microarrays much and I don't have the resources to
maintain tools we're not using.
I would be very happy to see the code taken over if anyone has the
resources but for now and will help any way I can.
(FYI: We've had some success using chipster for routine microarray
analyses from http://chipster.csc.fi/ although it's buggy and doesn't
seem to be very actively maintained)
On Mon, Jul 23, 2012 at 12:04 PM, Jon Manning <jonathan.mann...@ed.ac.uk> wrote:
> Hi all,
> My apologies if this seems obvious to many of you (seems like something that
> will have been dealt with)- but I've been rooting around in the docs and
> mailing list to no concrete avail.
> I'm looking to Galaxyise our existing (somewhat informal) microarray
> analysis workflows. I've found rexpression etc and the associated helpful
> datatypes. But I'm stuck at the import of .CEL files:
> Do I need to create a new datatype to represent .CEL? The fact this doesn't
> exist by default suggests it's not the right approach.
> Assuming I was to do the above, how would I create a function to generate an
> affyBatch (for example) from an unspecified number of input .CEL?
> Is the solution to have R work with a .tar and a config file to produce the
> affyBatch, thereby bypassing the .CEL requirement? But then there's no .tar
> datatype either.....
> If I've missed the docs I'm happy to be chided and pushed in the right
> Many thanks,
> Dr Jonathan Manning
> Bioinformatics Team
> Centre for Cardiovascular Science
> University of Edinburgh
> Queens Medical Research Institute
> 47 Little France Crescent
> Edinburgh EH16 4TJ
> United Kingdom
> T: +44 131 242 6700
> F: +44 131 242 6782
> E: jmann...@staffmail.ed.ac.uk
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
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