similar to: GridR error

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")

Dear All I am doing one distributed data mining program. So I selected GridR package for the distributed programming. *grid.init(service="local",debug=FALSE, localTmpDir="GridRTmp/") grid.apply("x",UCS, wait=TRUE )* UCS is a function. When I execute this statement, I have some errors like : *cannot load local function/variable: xmlRoot extracted from line: : no

Hello, I've been attempting to make a generic method that dispatches on the first argument, which can be either an S3 or an S4 class. This is as far as I've gotten. Any suggestions about what to try next ? library(aroma.affymetrix) library(GenomicRanges) setGeneric("analyse", function(x, y, ...) standardGeneric("analyse")) setMethodS3("analyse",

Hello, I'm trying to track down the cause of some extreme memory usage and I've been using Dirk Eddelbuettel's lsos() function he posted on stack overflow. There is a large difference between R's RAM usage : PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 6637 darstr 20 0 30.0g 29g 4712 S 0 63.2 10:34.43 R and what objects I have loaded in memory :

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5

Is there a way to estimate a nominal response model? To be more specific let's say I want to calibrate: \pi_{v}(\theta_j)=\frac{e^{\xi_{v}+\lambda_{v}\theta_j}}{\sum_{h=1}^m e^{\xi_{h}+\lambda_{h}\theta_j}} Where $\theta_j$ is a the dependent variable and I need to estimate $\xi_{h}$ and $\lambda_{h}$ for $h \in {1...,m}$. Thank you, Mauricio Romero Quantil S.A.S. Cel: 3112231150

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5

Hello dear R-help group (and David Smith from REvolution), I would like to perform parallel computing using R with Condor (hopefully using foreach or other recommended solutions, if available) for some "Embarrassingly parallel" problem. I will start by listing what I found so far, and then go on asking for help. So far I found the a manual by Xianhong Xie from Rnews_2005-2 (see page

Dear all I am implement one grid computing system using GridR package. I am working on windows platform. I did all the configuration according to the GridR tutorial. But it has some errors when I execute grid.apply function. Here is the output from stderr: R: not found java.io.IOException: Error during SCP transfer. at com.trilead.ssh2.SCPClient.get(SCPClient.java:703) at

Hello, I'm trying to use coxph() function to fit a very simple Cox proportional hazards regression model (only one covariate) but the parameter space is restricted to an open set (0, 1). Can I still obtain a valid estimate by using coxph function in this scenario? If yes, how? Any suggestion would be greatly appreciated. Thanks!!! [[alternative HTML version deleted]]

I've got two tables.... first one(table1): ID chrom start end Ex1 2 152 180 Ex2 10 2000 2220 Ex3 15 3000 4000 second one ( table2): chrom location name 2 160 Alv 2 190 GNN 2 100

Hello, I have start and end coordinates from different experiments (DNase hypersensitivity data) and now I would like to combine overlapping intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101 are combined to 30-101. But 49-101 and 70-103 would not be combined because they are on different chromosomes (chr a and chr b). Does anybody have an idea? Thanks Hermann > df

Hi everyone,   I'm trying to do an Logistic Politomic Regression in R. Because I have my resposes variables and the aswer is 0 and 1 in 3 bacterial genes. Somebody know how to do this in R in a easy way?   Thank so much,   José Bustos Facultad de Ciencias Universidad Catolica Ssma. Concepcion Chile --- El lun, 31/8/09, r-help-request@r-project.org <r-help-request@r-project..org>

I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and

I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and