Question: FW: bioconductor

0

Warnes, Gregory R •

**460**wrote:
[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]]
>
> _______________________________________________
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> 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
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