similar to: unable to compute MAD in aCGH package

Hi, I would like to analyze some agilent aCGH copy number files. As a start, I would like to normalize this data. I don't know what is the standard way to do this. Which package is the standard one that people use for this purpose? The chips that I am looking at are the agilent sure print 1M (G4447a) array and a custom chip with similar format. My raw data is a text file with spot locations

Hello everyone, I'm trying to open the same file under Linux and Windows. Under Windows everything is ok but when I try to do it under Linux I have a mistake and I don't know why. This is the mistake: Error in make.names(col.names,unique=TRUE): string multibyte 1 invalid why? I write this when I want to do it under Windows: zz.info<-read.table(file("C:/Documents and

Hello, I want to perform an lme on a database with this structure: ID Sequence Temperature Tumour Error 1 5 0 1 8.721872e-08 1 5 0 2 8.695348e-08 1 5 0 3 2.019604e-13 1 5 37 1

Dear all, I executed svm calculation using e1071 library with a microarray data (http://www.iu.a.u-tokyo.ac.jp/~kadota/R/data_Singh_RMA_3274.txt). Then, I shuffled the data samples and executed svm calculation again. The results of 2 calculation were different (in SV, coefs and weights). I attached the script below. Could please tell me why this happens? If possible please tell me how to make

I have what I *think* should be a simple problem in R, and hope someone might be able to help me. I'm working with cancer survival data, and would like to calculate adjusted survival figures based on the age of the patient and the tumour classification. A friendly statistician told me I should use Cox proportional hazards to do this, and I've made some progress with using the

Dear All. I have the following table that I want to analyze using multinom function freq segments sample 4271 Seg1 tumour 4311 Seg2 tumour 3515 Seg1 normal 3561 Seg2 normal I want to compare model with both factors to the one where only sample is present. model1=multinom(freq~segments+sample,data=table) model2=multinom(freq~ sample,data=table)

Dear all, I have a couple of questions regarding the survival:::cch function. 1) I notice that Prentice and Self-Prentice functions are giving identical standard errors (not by chance but by programming design) while their estimates are different. My guess is they are both using the standard error form from Self and Prentice (1986). I see that standard errors for both methods are

Hi friends, I need suggestions/directions on how to producing a waterfall plot for present extend of change in tumour size for a set of respondents in a study.  Example of use of waterfall plot is in the following slides presented at ASCO 2007 by Axel Grothey. Link is

Dear all, we have an exciting PhD position applying HPC to the analysis of large scale cancer datasets. The post will suit an applicant from a strong computational background who wishes to apply their knowledge to help develop a better understanding of the processes that control how tumours develop. Details below:- High Performance Computing applied to cancer research: Computational analysis of

Hola. Como te dijo Carlos, el problema está en los nombres de las columnas y en los nombres de las filas. Cuando hice la importación (con dd<-read.csv('mortality.csv'), tuve problemas con las filas de nombre: - Malignant tumour of the larynx trachea bronchus and lungs - Malignant tumour of the lip pharynx and mouth - Other endocrinological metabolic and nutritional conditions

Hello, I have the next function call: lme(fixed=Error ~ Temperature * Tumour ,random = ~1|ID, data=error_DB) which returns an lme object. I am interested on carrying out some kind of lsmeans on the data returned, but I cannot find any function to do this in R. I'have seen the effect() function, but it does not work with lme objects. Any idea? Best, Dani -- Daniel Valverde Saub? Grup

list.files() (and dir()) don't appear to return names of directories when one uses the recursive=T argument. E.g., > dir(file.path(R.home(),"library"), pattern="^R$", recursive=T) [1] "Malmig/help/R" but the unix find commmand finds lots of R directories > z <- system(paste("find", file.path(R.home(),"library"), "-name

Hello, since Bioconductor devel branch 3.11 started, which is operating with R-devel 4.0.0 (for e.g. 2019-11-03 r77362 on OS X 10.11.6 El Capitan), my package CFAssay 1.21.0 is not built on none of all three Systems, Linux, Windos and Mac. The error message refers to xy.coords which is called by R function plot.default. I found out that it has to do with the S3 object system. In my package I

On 15/11/2019 8:42 a.m., Herbert Braselmann wrote: > Hello, > > since Bioconductor devel branch 3.11 started, which is operating with > R-devel 4.0.0 (for e.g. 2019-11-03 r77362 on OS X 10.11.6 El Capitan), > my package CFAssay 1.21.0 is not built on none of all three Systems, > Linux, Windos and Mac. The error message refers to xy.coords which is > called by R function

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Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

Hi all, I'm new to R and I'm struggling to decipher an error message. Briefly, I am trying to use the pvclust package to do hierarchical clustering of some CGH data. The data is from the Progenetix CGH database. It is arranged as a table where each column is a single case and each row is a single chromosome band. The value in each cell is either 0, 1, 2, or -1. Corresponding to no change,

Hi, The following code, from Angelo Canty article on line "Resampling Methods in R: the boot Package, 2002", works fine for Angelo Canty using R 2.6.0 on Windows XP. It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after installing the S-PLUS bootstrap library, with slight differences in my outputs. > library(boot) > library(survival) >

Hi, The following code, from Angelo Canty article on line "Resampling Methods in R: the boot Package, 2002", works fine for Angelo Canty using R 2.6.0 on Windows XP. It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after installing the S-PLUS bootstrap library, with slight differences in my outputs. > library(boot) > library(survival)

Hello all, I posted a question to this list last week and received no response. I am unsure if this means no-one knows the answer or if I posed the question badly. I'm going to assume I posed the question badly and try again. I am new to R so it is quite likely it's a very naive question, however if there is something blindingly obvious that I am missing or if there is another resource I