## User: kpollard

kpollard •

**110**- Reputation:
**110**- Status:
- Trusted
- Location:
- United States
- Last seen:
- 13 years, 7 months ago
- Joined:
- 14 years, 2 months ago
- Email:
- k****************@gladstone.ucsf.edu

#### Posts by kpollard

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... It sounds like you have a lot of hypotheses and that after multiple testing adjustment all non-zero unadjusted p-values become 1s, which is probably the correct output of the maxT procedure. It is designed to control family-wise error, so will increase p-values a great deal when you have many tests. ...

written 3.4 years ago by
kpollard •

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... Hi Eric - It indeed looks like you've hit the memory limit. The object my.dist that you are attempting to create is a vector of length 610758*610757/2.
Best,
Katie
...

written 4.0 years ago by
kpollard •

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... Hi Yun,
Did you download hopach from CRAN or from BioC? The version on CRAN is
for
general use (not specifically arrays) and therefore does not include
some
of the array-specific funcitons like hopach2tree. If you have this
one,
try installing the version from BioC. If this isn't the problem, let
m ...

written 13.6 years ago by
kpollard •

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... FYI: the dendogram that is made with Stefano's code is the usual
binary
hierarchical tree from hclust, but using the new distance function
(eg:
disscosangle). At this time, it is not possible to view the hopach
hierarchical tree (which is non-binary) with heatmap. However, the
function hopach2tree i ...

written 13.8 years ago by
kpollard •

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... Haiyan,
There are actually two problems with the code below. One is easy to
fix
and relates to how you are defining the data. Try this instead:
group<-rep(0:1,5)
For test="f.block", it is necessary to input the data by block, with
observations within block labelled 0:(k-1), where k is the numb ...

written 13.9 years ago by
kpollard •

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Answer:
A: multtest problem...

... Jo,
The statistic is the same between multtest and t.test (for t-tests) or
wilcox.test (for wilcoxen tests), but the p-value is computed
differently.
The functions in t.test and wilcox.test use tabled distributions to
get a
p-value for each test. These assume a certain distribution for the
test
st ...

written 14.0 years ago by
kpollard •

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... Hi Benjamin,
Jim gives a good answer to your question. The MTP function uses a
bootstrap null distribution to compute p-values for Cox regression
coefficients (permuation null distribution is available for t- and
F-tests, but not Cox or linear regression). If your arrays are iid and
your sample siz ...

written 14.0 years ago by
kpollard •

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... Hello All,
I've just found and fixed a bug in the boot.resample function of the
multtest package. This function is called by the function MTP. So, if
you
have been using the MTP function with multtest version 1.5.x, you may
have
incorrect p-values (rawp and adjp). Other functions, such as mt.minP,
...

written 14.1 years ago by
kpollard •

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... Ken recently posted a question to the list regarding computation of t-
and
F-statistics (and corresponding unadjusted p-values) in multtest. Here
are
some suggestions.
Ken's data set consists of the following:
m: a 22277x6 matrix of probeset expressions
m.cl=c(0,0,0,1,1,1): the corresponding class ...

written 14.1 years ago by
kpollard •

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... Hi Anthony,
I believe that this bug has been fixed. Please try the "development"
version of hopach (v1.0.2):
http://www.bioconductor.org/repository/devel/package/html/hopach.html
Let me know if the problem persists.
Cheers,
Katie
> Date: Mon, 14 Mar 2005 07:38:45 +0100
> From: Anthony Bo ...

written 14.1 years ago by
kpollard •

**110**#### Latest awards to kpollard

Scholar
4.0 years ago,
created an answer that has been accepted.
For A: HOPACH error: "negative length vectors are not allowed" in distancematrix(). Mat

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