[BioC] bioconductor
A.J. Rossini
rossini at blindglobe.net
Wed Nov 19 16:49:47 MET 2003
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 at 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 at blindglobe.net [mailto:rossini at blindglobe.net]
>> Sent: Wednesday, November 19, 2003 9:51 AM
>> To: Roger Vallejo
>> Cc: bioconductor at 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 at 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 at psu.edu <mailto:rvallejo at psu.edu>
>> >
>> > Website: http://genomics.cas.psu.edu/
> <http://genomics.cas.psu.edu/>
>>
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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>>
>
> --
> rossini at 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
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--
rossini at 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
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