Question: MTP bug
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gravatar for kpollard
14.4 years ago by
kpollard110
United States
kpollard110 wrote:
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 number of observations per block. If you make this change, then you can run the permuation MTP: m1<-MTP(X=data,Y=group,test="f.block",alternative="less",B=100, method="sd.minP",nulldist="perm") This function calls mt.minP with classlabel=Y. From the documentation: classlabel: A vector of integers corresponding to observation (column) class labels. For k classes, the labels must be integers between 0 and k-1. For the 'blockf' test option, observations may be divided into n/k blocks of k observations each. The observations are ordered by block, and within each block, they are labeled using the integers 0 to k-1. The second problem is actually a bug in MTP with the bootstrap null distribution. When the number of observations per block is very small (2 here), then it is easy to get a bootstrap sampled data set with missing data in one or more blocks. I need to think about how to handle this. I will email again when a fix has been posted on the developmental packages section of bioconductor.org. Thanks for noticing the problem! Katie > Date: Fri, 10 Jun 2005 18:09:49 +0800 > From: "Haiyan Pan" <hypan at="" scbit.org=""> > Subject: [BioC] bug for MTP > To: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <200506101010.j5AAAe14008147 at hypatia.math.ethz.ch> > Content-Type: text/plain; charset="gb2312" > > bioconductor: > > when I used the following example to do MTP analysis > > > #data > set.seed(99) > data<-matrix(rnorm(90),nr=9) > group<-c(rep(1,5),rep(0,5)) > > m1<-MTP(X=data,Y=group,test = "f.block",alternative="less",B=100,method="sd.minP") > > the following error information occurs: > > Error in "[<-"(`*tmp*`, (i - 1) * l + j, value = numeric(0)) : > nothing to replace with > In addition: Warning messages: > 1: number of items to replace is not a multiple of replacement length > 2: number of items to replace is not a multiple of replacement length > 3: number of items to replace is not a multiple of replacement length > 4: number of items to replace is not a multiple of replacement length > > how to fix it? Thanks
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