## User: Sandrine Dudoit

Sandrine Dudoit •

**170**- Reputation:
**170**- Status:
- Trusted
- Location:
- Last seen:
- 14 years, 11 months ago
- Joined:
- 16 years, 6 months ago
- Email:
- s*******@stat.berkeley.edu

#### Posts by Sandrine Dudoit

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Answer:
A: Software for clest?

... Hi Peter,
Thanks for your interest in Clest. Unfortunately, we do not have
software
for this.
Best regards,
Sandrine
----------------------------------------------------------------------
---------
Sandrine Dudoit, Ph.D. E-mail:
sandrine@stat.berkeley.edu
Assistant Professor ...

written 15.0 years ago by
Sandrine Dudoit •

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Answer:
A: Westfall and Young "maxT"

... Hello,
> I've got a question regarding the Westfall and Young "maxT"
procedure
> (implemented in Bioconductor package multtest, function mt.maxT).
>
> If one calculates a two sample T-statistic assuming unequal
variances
> for the groups, then the resultant statistic is only approxim ...

written 15.3 years ago by
Sandrine Dudoit •

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Answer:
A: multtest

... Hi Stefanie,
Thank you for the feedback. We have updated the code and fixed
the help pages to clarify the issues you raised about the computation
of the Wilcoxon test statistic. The revised package is available
under "Developmental Packages".
Below are answers to your three questions.
> 1. Wha ...

written 15.4 years ago by
Sandrine Dudoit •

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... Hello,
If you are a windows user, you should download the windows version of
the
package available at
http://www.bioconductor.org/workshops/EMBO03/embo03.html
You can then use standard R installation procedures described in the R
manuals or FAQ
http://www.r-project.org
Best regards,
Sandrine
-- ...

written 15.4 years ago by
Sandrine Dudoit •

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Answer:
A: beginner question

... Hi Matthew,
Wish I had time to cover more material during the EBI workshop ...
Instructions for installing R and Bioconductor are given in the FAQ
http://www.bioconductor.org/faq.html#How can Bioconductor be obtained
The slides and labs for the EBI and other courses are posted in the
"Short
Cours ...

written 15.5 years ago by
Sandrine Dudoit •

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Answer:
A: Multtest Question!

... We used Gaussian p-values simply as an example.
You can use the function mt.maxT to obtained permutation unadjusted
p-values as well as adjusted p-values.
In general, the Gaussian p-values should be adequate when you have
fairly large sample sizes in both groups, so that AVERAGES in both
groups are ...

written 15.7 years ago by
Sandrine Dudoit •

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Answer:
A: SVM

... Hi Pam,
The e1071 and other classification packages can be downloaded from
CRAN
http://cran.r-project.org/.
Best,
Sandrine
On Tue, 17 Dec 2002, Pamela Wolfe wrote:
> I have recently downloaded R and bioconductor. There were several
Classification Packages listed in the handout that accompanie ...

written 15.8 years ago by
Sandrine Dudoit •

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516

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Answer:
A: Swirl Data

... Hi Jason,
Use <- instead of <-- for the assignment operator.
Sandrine
On Fri, 6 Dec 2002, Jason Skelton wrote:
>
> Hi
> I'm having difficulty with accessing the swirl(zebrafish) data
> from the document about Bioconductor's marrayNorm package
> (Dudoit, Yang Aug 2002)
> I ...

written 15.9 years ago by
Sandrine Dudoit •

**170**0

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705

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Answer:
A: Help with raw p-value

... Hi,
The p-values in rawp0 are calculated based on a standard normal
distribution, while those in t.test are calculated based on a
t-distribution with df = 11.049.
Try
2*(1-pt(abs(teststat[1]),df=11.049))
and you will get the same p-value as with t.test.
Sandrine
--------------------------------- ...

written 16.0 years ago by
Sandrine Dudoit •

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423

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Comment:
C: problem in diagnostic plots?

... Yes, the problem is with how we set widths and heights in the layout
function. Some combinations work on some computers but not others. We
will try to sort this out.
Sandrine
On Wed, 31 Jul 2002, Joshua Betcher wrote:
> The problem lies with the use of the "layout" function within
maDiagnPlots ...

written 16.2 years ago by
Sandrine Dudoit •

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