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]]

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}}

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}}

Sounds great, I'm looking forward to the contributed vignettes! (this is a general suggestion, not just to Greg -- user contributions of this form would be invaluable to this project) best, -tony "Warnes, Gregory R" <gregory_r_warnes@groton.pfizer.com> writes: > 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 message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. > -- 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}}

At 02:39 AM 20/11/2003, Warnes, Gregory R wrote: >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 limma vignette does this. By the way, I think your suggestions are great, and I'd dearly like a better overview intro to BioC, but fulfilling all the asks below would fill a two volume book and would make the authors famous! Gordon >[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 ...

> -----Original Message----- > From: Gordon Smyth [mailto:smyth@wehi.edu.au] > Sent: Wednesday, November 19, 2003 5:31 PM > To: Warnes, Gregory R > Cc: 'rossini@u.washington.edu'; Roger Vallejo; > bioconductor@stat.math.ethz.ch > Subject: RE: [BioC] bioconductor > > > At 02:39 AM 20/11/2003, Warnes, Gregory R wrote: > > >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 limma vignette does this. Great, I'll take a look. > > By the way, I think your suggestions are great, and I'd dearly like a > better overview intro to BioC, but fulfilling all the asks > below would fill > a two volume book and would make the authors famous! So we need to make it a collaborative effort so that we can all make more $$ and become famous! -G > > Gordon > > >[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 > > ... > LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}

I would love to see a comprehensive manual like that. It would be very helpful for biologists. And I believe it is better to disseminate this manual online rather than as a printed text. Before this, it would be nice to have a vignette that contains a flowchart of a typical microarray analysis steps and the applicable libraries like the one in the short courses for the time being. The chart should be followed by the short descriptions of the functionalities of the libraries. Then one can have a quick overview of the bioconductor libraries in just one vignette, and can choose the suitable library for a particular analysis without browsing through all the vignettes. Regards, Fai _______ Yuk Fai Leung Bauer Center for Genomics Research Harvard University 7 Divinity Avenue Cambridge, MA 02138 Tel: 617-496-7134 Fax: 617-495-2196 email: yfleung@cgr.harvard.edu; yfleung@genomicshome.com URL: http://genomicshome.com <http: genomicshome.com=""/> > ------------------------------ > > Message: 5 > Date: Thu, 20 Nov 2003 09:31:27 +1100 > From: Gordon Smyth <smyth@wehi.edu.au> > Subject: RE: [BioC] bioconductor > To: "Warnes, Gregory R" <gregory_r_warnes@groton.pfizer.com> > Cc: "'rossini@u.washington.edu'" <rossini@u.washington.edu>, Roger > Vallejo <rvallejo@psu.edu>, bioconductor@stat.math.ethz.ch > Message-ID: <6.0.1.1.1.20031120092602.02938a88@imaphost.wehi.edu.au> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > At 02:39 AM 20/11/2003, Warnes, Gregory R wrote: > > >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 limma vignette does this. > > By the way, I think your suggestions are great, and I'd dearly like a > better overview intro to BioC, but fulfilling all the asks below would > fill a two volume book and would make the authors famous! > > Gordon > > >[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 > > ... > ________ Yuk Fai Leung Bauer Center for Genomics Research Harvard University 7 Divinity Avenue Cambridge, MA 02138 Tel: 617-496-7134 Fax: 617-495-2196 email: <mailto:yfleung@cgr.harvard.edu> yfleung@cgr.harvard.edu; <mailto:yfleung@genomicshome.com> yfleung@genomicshome.com URL: <http: genomicshome.com=""> http://genomicshome.com [[alternative HTML version deleted]]