Question: How To Set Up A Microarray Analysis Workflow In Galaxy?
8.2 years ago by
Yury Bukhman • 140
Yury Bukhman • 140 wrote:
Hi, I am new to Galaxy. My co-workers have installed a Galaxy server locally and written wrappers for a couple of command-line programs. Now I would like to implement a microarray data analysis workflow using R and Bioconductor. I imagine, it would have the following steps: 1) A user uploads a set of files that constitute a microarray experiment, e.g. a bunch of Affymetrix CEL files and a spreadsheet of information that describes experimental conditions (to be imported into the phenoData slot of a Bioconductor ExpressionSet object) 2) An R script is run to parse/normalize/summarize the data and generate and ExpressionSet object. This object is stored as a file. 3) Another R script takes the ExpressionSet as its input and does some downstream analysis using appropriate Bioconductor packages I have the following questions. My apologies if they are trivial, as I am a novice here: 1) How do I enable a non-administrative user upload a dataset that consists of multiple files, for the first step of my workflow? 2) Will Galaxy store an .RData file? 3) Are there any other issues that I should know about before I plunge into this? Thanks Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: firstname.lastname@example.org
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