similar to: R function for Gap statistic

Dear mailing group, This is my first time here. Glad to have this resource! I am currently trying to load an Excel file into R (limma package loaded) using the source(*name of directory*) command, but it cannot open the file. I renamed the file as .R and .RData, to no avail. The Excel data contains one gene name per row and about 100 data points per gene (columns). I am only used to

Has anyone implemented Tibrishani's gap statistic in R or S plus? If so I would greatly appreciate the relevant script file. Any help will be much appreciated Kind regards Dr Graham Leask Economics and Strategy Group Aston Business School Aston University Aston Triangle Birmingham B4 7ET Tel: Direct line 0121 204 3150 email g.leask@aston.ac.uk [[alternative HTML version deleted]]

the following code apprantely, for some grand old reason, induces a syntax error: if (seq[i] = "A") m <- trans[1,] where seq is a vector and trans is a matrix. I cannot for the life of me see why this is wrong. Syntax error is: Error: syntax error in "if (seq[i] =" Sincerely, Norman Goodacre ---------------------------------

Dear help group, Just fyi a markov chain is a sequence of transitions between states (say A,T,G,C - on a gene) with a given probability for each transition. In this case there'd be 16 different kinds, each with a different weight. Given a transition matrix (4x4) filled with all transition probabilities of course, how can I generate a random sequence of a given length, say 200?

Dear group, I am nearly beside myself. After an entire night spent on a niggling little detail, I am no closer to to the truth. I loaded an Excel file in .csv form into R. It apparentely loads as a list, but not the kind of list you can use. Oh no, it converts into a list that cannot be converted into an integer, numeric, or vector, only a matrix, whihc is useless without integers.

Dear R mailing group, The second parameter for the function optim()is a function whose parameters are to be optimized. The description of this function given in the help file is the following: fn: A function to be minimized (or maximized), with first argument the vector of parameters over which minimization is to take place. It should return a scalar result.

Dear R mailing group, I am having extreme - and mysterious - trouble installing R. I tried simply dl ing R-2.3.1.tar.gz, and unzipping it, but after doing so, nowhere could I find a file called R-2.3.1.exe. I did however find an R-2.3.1.exe.manifest. I therefore tried the command line installation command - given in R-admin.pdf. This command is: tar zxvf R-2.3.1.tgz This is strange

Hi, I am having trouble compiling package gap http://www.hgmp.mrc.ac.uk/~jzhao/r-progs.htm on Tiger. I have installed XcodeTools 2.1. The binary version of gap currently available on CRAN has some bug and is fixed in the latest version. The message I get from R is below. Any help is greatly appreciated. best regards, Kenny Ye tar: Read 1536 bytes from - * Installing *source* package

I am trying to do a simple segregation analysis using the GAP package. I have the documentation for pointer but I desperately need an example so that I can see how to format the datfile and the jobfile. For each individual, I have FamilyId, SubjectId, FatherId, MotherId, and AffectedStatus (0/1). I would like to obtain the likelihood ratio statistic for transmission. I would greatly

Hello! Using the package Plotrix I want to do a plot with a broken axis. So far it's working fine but now I want only the x and y axis plotted (the x-axis with a gap in it), but not the axes that are reffered to as axis 3 and 4, and not the lines that additionally mark the gap in the axis. I thought an 'axes=F' in the gap.plot() command would do (as in the usual plot()), but it does

I am trying to create a boxplot that has a gap with different scales so that my boxes actually show (compare attachments). I have referred to the help pages for gap.boxplot, gap.plot, list with no luck so far. Here is my script and the resulting error message: # Import *.csv files containing areas for each CLI class cli3<-read.table("F:\\Megan\\cli3.csv", header=TRUE,

I am trying to make a barplot with a broken axis using gap.barplot (in the indispensable plotrix package). This works well when the data is a vector: > twogrp<-c(rnorm(10)+4,rnorm(10)+20) > gap.barplot(twogrp,gap=c(8,16),xlab="Index",ytics=c(3,6,17,20),ylab="Group values",main="Barplot with gap") But when the data is an array (for a bar plot with multiple

Hi My question is simple - the gap.plot function in the plotrix package allows users to draw graphs that have a broken axis. However, I want to then add a line to the "second" plot, but can't. Eg: twogrp<-c(rnorm(10)+4,rnorm(10)+20) gap.plot(twogrp,rnorm(20),gap.bounds=c(8,16),gap.axis="x",xlab="X values", xtics=c(4,7,17,20),ylab="Y

Dear mailing group, I have loaded an Excel file into R by calling it ".csv" and using the "read.csv" function in R. However then I want to use the (limma package specific, I believe) function "hclust", which clusters data in a tree dendrogram, by similarity. However, I receive the errors msg.s: 1) "missing observations in cov/cor" 2) "In

Hi, all I am trying to make a plot with a axis break and I want the whole plot to be line, not points. However, when I execute the following command half of the graph is points and the other lines. gap.plot(Xdata, Ydata,gap=c(5,6),gap.axis="x",type="l") I think it might be a bug in plotrix. I would greatly appreciate your input. If there is another way to do it, I

Hi everyone. I'm trying to break the y axis on a plot. For instance, I have 2 series (points and a loess). Since the loess is a "continuous" set of points, it passes in the break section. However, with gap.plot I cant plot the loess because of this (I got the message "some values of y will not be displayed"). Here's my code: library(plotrix); #generate some data x

Dear all: I have the following codes: Xdata<-c(2,3,8,9,10) Ydata<-1:5 gap.plot(Xdata, Ydata,gap=c(5,6),gap.axis="x",type="o") However, the type='o' seems only work on the first part of gap plot, the second half of the plot always just points, you can not add lines on that part, any help will be highly appreciated. I would like to have these two parts of

I am getting an unexpected gap in a simple plot of monthly data series. I have created a csv file of monthly climate observations that I store on-line. When I download the csv file and plot one of the series, I get a gap even though there is data for the missing point. Here is a snippet to show the problem. ## Strange plot results link <-

I have a time series of about 1500 measurements. There are sporadic data gaps. I would like to plot the time series with type "line". I only want a line to connect the periods with data; I don't want a line to connect the points across a data gap. Is there a function or recommended method to deal with this? For example there are 2000 days days 1:1000 each have one

Dear R users, I did install R. 2.0.1, and try to load "gap" package. However, below is the message shown when I did load it. Can anybody please let me know my mistakes? ---- > library() > library(gap) Loading required package: MASS Loading required package: genetics Loading required package: combinat Loading required package: gdata Error: package 'gdata' could not be