[Paul is a new poster, so I'm forwarding this until he gets posting approval..] -----Original Message----- From: Paul Grosu [mailto:Grosu@CGR.Harvard.edu] Sent: Wednesday, November 19, 2003 11:01 AM To: 'Warnes, Gregory R'; 'rossini@u.washington.edu'; 'Roger Vallejo' Cc: 'bioconductor@stat.math.ethz.ch' Subject: RE: [BioC] bioconductor Hi - I just signed up to the list and don't know if anyone posted this already but I'm providing a link to Chis Bye's "A Biologist's Guide to using Bioconductor" - it's not long: http://www.fas.harvard.edu/~grosu/downloads/bioconductor_manual.pdf This is in no way will cover the completeness of Greg's list but might be a good starting point. Paul Grosu Bioinformatician Bauer Center for Genomics Research/Harvard University -----Original Message----- From: Warnes, Gregory R [mailto:gregory_r_warnes@groton.pfizer.com] Sent: Wednesday, November 19, 2003 10:39 AM To: 'rossini@u.washington.edu'; Roger Vallejo Cc: bioconductor@stat.math.ethz.ch Subject: RE: [BioC] bioconductor We talked about this at the BioCBUG meeting a couple of weeks ago. The web site does have clear instructions for *installing* Bioconductor, it is just not clear what to do once it is installed. I think that the necessary documentation is available, but it is fragmented: 1) It is not clear from the web site what documentation you need to read to get started. 2) None of the vignettes that I've looked at show a complete analysis session from start to finish. [I think the reason for this is that the people writing the vignettes are the *package* authors and they have slightly different interests from *consumers*] I would suggest 1) Adding a topic on the front page and on the navbar "Getting Started with Bioconductor" that brings up a page with a small number of vignettes titled like: Getting Started with Affymetrix Data Getting Started with Custom Two-Channel Data Getting Started with XXXXX Data ... These vignettes should go through an common-case example analysis from start to finish. From my work the flow should be something like this for Affymetrix data: 1) Prerequisites - Software: R, Bioconductor - Data: CEL files, experiment information - install the required CDF package 2) Load the data 3) Perform standard (technology) Quality Control tests - 3'/5' ratios - Chip images - RNA digestion plots 4) Normalize/scale/standardize the data 5) Perform 'overall' visualizations - MDS and PCA for samples using all probesets 6) Apply a statistical model to all probesets - ANOVA / ANCOVA - Contrasts 7) Apply multiple comparison correction (FDR, ...) 8) Filter based on statistical model - Select probesets with FDR < 0.05 [Note that I didn't metion filtering earlier, I think it is a bad idea to filter before applying a model!] 9) Add annotation 10) Generate visualizations - PCA/MDS for samples using statistically significant genes - Profile plots across experimental conditions / treatments - heatmap including 2-way hirarchical clustering 11) Generate tabulations - Table of top XX results from statistical model with subset of annotation 12) Generate output dataset for interactive visualization in Spotfire/Excel/... - All results from statistical model with all annotation For the getting started document I would recommend giving the *simplest* good-practice method of accomplishing each task. Each section should also include a pointer to other documents that can provide further details on how the alogrithms work / alternative commands / etc. -Greg > -----Original Message----- > From: rossini@blindglobe.net [mailto:rossini@blindglobe.net] > Sent: Wednesday, November 19, 2003 9:51 AM > To: Roger Vallejo > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] bioconductor > > > > You aren't being helpful or explicit. 3-4 hours doing what? What > exactly have you read? How do you expect us to suggest things when > you don't tell us what you've done? > > > But more importantly, have you tried > > library(tkWidgets) > vExplorer() > > and looked at the affy vignettes? > > > > "Roger Vallejo" <rvallejo@psu.edu> writes: > > > DO you have a manual that shows how to learn to use BIOCONDUCTOR? > > > > I have spent 3-4 hrs and I see only lots of bla bla bla but > any direct > > instructions on how to start loading affy genechip data and > performing > > rudimentary microarray data analysis. > > > > Many thanks in advance for the help.. > > > > Roger > > > > > > > > > > > > Roger L. Vallejo, Ph.D. > > > > Assist. Professor of Genomics/Bioinformatics > > > > The Pennsylvania State University > > > > Department of Dairy & Animal Science > > > > Genomics & Bioinformatics Laboratory > > > > 305 Henning Building > > > > University Park, PA 16802 > > > > Phone: (814) 865-1846 > > > > Fax: (814) 863-6042 > > > > Email: rvallejo@psu.edu <mailto:rvallejo@psu.edu> > > > > Website: http://genomics.cas.psu.edu/ <http: genomics.cas.psu.edu=""/> > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}} _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}} _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}