Hi, Jon. 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.Manning@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 direction.
Many thanks,
Jon
-- 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: jmanning@staffmail.ed.ac.uk
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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