similar to: Generelized Negative Binomial model in R

Hello ; I am doing a regression of count data (number of award and there are some covariates) I have estiamted the parameters of negative binomial distribuion (lambda is a function of covaraites, GLM model) by glm.nb function and training dataset. Now I want to predict the number of award (for example y=0, y=1, y=2,) or testing dataset. I dont know how to calculate this numbers? I would be very

Hello I am running a project but I encounter a problem . I would be happy to receive help : problem: I have a binary dependent variable and some covariates logit(y)=a+bx+cz . I want to estimate the score vectors and their covariance by the usage of logit function and so glm in R .The vlaue of one of the coefficient ( like b) is known previously and I want to extract a and c and covariance

I am looking for code that allows for a more flexible negative binomial model (similar to Stata's "gnbreg"). In particular, I am looking to be able to model the ancillary shape parameter in terms of a series of covariates. So if, y[i] ~ poisson(mu[i]) mu[i] = exp(x[i]beta + u[i]) exp(u[i]) ~ Gamma(1/alpha, alpha) I am looking to parameterize alpha as exp(z[i]gamma). If you

Dear list, How can I detect a package is installed or not? If not, then install it. For example, in a script, I want to check the package DESeq is installed or not. If not, then I will using this script to install it. source("http://www.bioconductor.org/biocLite.R") biocLite("DESeq") The pseudo script would be like this: try: library("DESeq") catch:

HI, I would like to update my DESeq package version on R-2-14 using bioclite() and get this message, could somebody help please? > biocLite("DESeq") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'DESeq' Installing package(s) into ?/nfs/team82/nac/R-modules? (as ?lib? is unspecified) trying URL

In your particular case I don't think that censoring is an issue, at least not for the reason that you discuss. The basic censoring assumption in the Cox model is that subjects who are censored have the same future risk as those who were a. not censored and b. have the same covariates. The real problem with informative censoring are the covaraites that are not in the model; ones that

Hello, I have RNAseq data, which I am trying to analyze with DESeq. My file (tab delimited .txt) appears to be correct: >head(myfile) VZ_w13 VZ_w14a VZ_w14b VZ_w15a VZ_w15b VZ_w16a ENSG00000253101 0 0 0 0 0 0 ENSG00000223972 0 0 0 0 0 0... However, when I try to analyze the data with >cds <-

Hello, Sorry if this question has been posted before but could't find out exactly an answer to the question.... I'm doing bioinformatics and doing small RNA sequencing that make use of packages such as DESeq and EDGE. For those familiar with this data you will notice that you end up having large matrices with millions of entries. So i guess many people might be facing the same problem

I have a data frame like this: T0h T0.25h T0.5h T1h T2h T3h T6h T12h T24h T48h C0h C0.25h C0.5h C1h C2h C3h C6h C12h C24h C48h NM_001001130 68 95 56 43 66 62 68 90 63 89 65 85 58 49 81 49 76 73 48 77 NM_001001152 79 129 52 50 24 45 130 154 112 147 56 85 67 33 52 31 93 77 65 109 ...

Greetings! We are trying to obtain confidence and prediction intervals for a predicted Y value from bootstrapped linear regression using the boot function. Does anyone know how to code it? Greatly appreciated. Janh [[alternative HTML version deleted]]

I know others have asked similar questions to the R developers, but I could not find the solution to this question. Please forgive me if I have missed a crucial point in a previous post. I would like to submit a package to CRAN that depends on the bioconductor package "edgeR". Listing "edgeR" under the Depends or Imports lines in the DESCRIPTION file for my package causes an

Hi, R-help, I have a group of data from RNA-seq want to be analyzed by Fisher's exact test in R. I want to compare the significant difference of about 30,0000 individuals in two different samples, and I have no idea how to use R, so could you please give me some suggestions or the scripts for Fisher's exact test? Thank you very much. Best, Guanfeng Wang [[alternative HTML version

Hi: I am using the package "KernSmooth" to do the local polynomial regression. However, it seems the function "locpoly" can only deal with univariate covaraite. I wonder is there any kernel smoothing package in R can deal with bivariate covariates? I also checked the package "lcofit" in which function "lcofit" can indeed deal with bivariate case. The

I am running and analysis of sequencing data uisng the EdgeR package. I have received the following error: Using grid search to estimate tagwise dispersion. Error: cannot allocate vector of size 307.3 Mb indicating the memory allocation is too small. How would I change this confiuration in R so that the script can run with the files I have? Help appreciated, Josquin -- View this message in

Thanks for all your great answers. The app I?m working on is indeed an exploratory data analysis tool for gene expression, which requires a bunch of bioconductor packages. I guess for now, my best solution is to divide my app into modules and load/unload packages as the user switch from one module to another. This brought me another question: it seems that unload package with the

Dear all, I'm writing to ask for advice as to best practice. A PhD student working with me is writing C++ code that we hope to make public as src code in our Bioconductor package edgeR. He wants to call the function fmm_spline, which is part of the source code for the stats package http://svn.r-project.org/R/trunk/src/library/stats/src/splines.c, from his C++ code. This function

Hello, all, I'm a new R user (new to any programming language in general, really), so I apologize if this is easy/has already been answered (I've attempted searching online but did not understand the pages I found). My data is stored in text files with the headers LANE, RNA_NAME, SEQ, and SEQCNT. I've been using x = "filename.txt" y = aggregate(x$SEQCNT, list(x$RNA_NAME),

https://bugs.freedesktop.org/show_bug.cgi?id=98457 Bug ID: 98457 Summary: [NVD9] GPU lockup after resume from hibernation with Nouveau driver and firmware-nonfree Product: xorg Version: unspecified Hardware: Other OS: All Status: NEW Severity: normal Priority: medium

CRAN (and crantastic) updates this week New packages ------------ * disclapmix (0.1) Maintainer: Mikkel Meyer Andersen Author(s): Mikkel Meyer Andersen and Poul Svante Eriksen License: GPL-2 http://crantastic.org/packages/disclapmix disclapmix makes inference in a mixture of Discrete Laplace distributions using the EM algorithm. * EstSimPDMP (1.1) Maintainer: Unknown Author(s):

Hi, I have quite a problem right now. After finish of development I installed rails with fcgi and apache on my production env. Everything seems to be configured ok, but once I while I get the famous error message: " Premature end of script headers: dispatch.fcgi" I cant see any generel configuration problem, as sometimes everything is running fine. Maybe it is a problem related to