User: kpollard

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kpollard110
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k****************@gladstone.ucsf.edu

Posts by kpollard

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Not getting Adjusted p-values from multtest package
... 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 3.6 years ago by kpollard110
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Answer: A: HOPACH error: "negative length vectors are not allowed" in distancematrix(). Mat
... 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 4.2 years ago by kpollard110
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About Hopach package
... 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 ...
hopach written 13.8 years ago by kpollard110
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How to use distance functions from hopach package in a heatmap?
... 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 ...
hopach written 14.0 years ago by kpollard110
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MTP bug
... 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 14.0 years ago by kpollard110
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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 14.1 years ago by kpollard110
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Cox MTP question
... 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 ...
microarray regression multtest written 14.2 years ago by kpollard110
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multtest bug fixed
... 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, ...
multtest written 14.2 years ago by kpollard110
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multtest Paired T-test
... 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 ...
multtest written 14.2 years ago by kpollard110
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(no subject)
... 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 ...
hopach written 14.3 years ago by kpollard110

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Scholar 4.2 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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