similar to: edgeR: design matrix setup

Hi all, I want to plot a facet plot with column names as x and column values as y. One plot for each row. here is part of my dataset: Gene T0h T0.25h T0.5h T1h T2h T3h T6h T12h T24h T48h NM_001001130 68 95 56 43 66 62 68 90 63 89 NM_001001144 0 1 4 0 1 1 1 4 1 2 NM_001001152 79 129 52 50 24 45 130 154 112 147 NM_001001160 1 1 2 0 0 1 0 0 0 1 NM_001001176 0 0 0 0 0 0 0 0 0 0 NM_001001177

hello folks, i am learning R and microarray analysis from scratch using different sites. today i am doing an exercise from http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#R_functions the section i am at is 2. Affymetrix data analysis. I understand the syntax given in this section up until: design <- model.matrix(~ -1+factor(c(1,1,2,2,3,3))) # Creates appropriate design

Hello, I am having trouble asking R to read individual numeric vectors for a box plot of the residuals of a linear regression. It is performing arithmetic addition on the 16 individual variables that I want individual box plots for. I have 16 race*treatment variables that were created from cleaned data.frames for race and treatment independently: t1W, t1B.....t4W, t4B, t4H, t4O. class(t1W)

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

Hello; Does anybody knows that R have a function for Generelized Negative Binomial model, something like "gnbreg" in "STATA" where dispersion parameter itself is a function of covaraites ? Thanks; [[alternative HTML version deleted]]

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

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),

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 R-Users, Are there any packages that enable the modifications of highlighted areas / annotations in pdf documents? It seems feasible - I have explored some R code (see below). However, I would rather avoid to reinvent the wheel. The problem: When highlighting pdf-documents with Microsoft Edge, the bounding box is sometimes misplaced, and quite ugly so. It also lacks the ability to draw

Hi, I have a few corrections for OPENssh-2.9p1 solaris packaging. I use to configure: setenv CFLAGS -I/opt/local/include setenv LDFLAGS "-R/opt/JGMAzlib/lib -L/opt/JGMAzlib/lib" ./configure --prefix=/opt/OPENssh --with-tcp-wrappers --sysconfdir=/etc/opt/OPENssh --localstatedir=/var/opt/OPENssh --with-pid-dir=/var/opt/OPENssh/run --with-ssl-dir=/opt/OPENssl --with-ipv4-default

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

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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):

Signed-off-by: Scott Seago <sseago at redhat.com> --- AUTHORS | 17 ++++++ README | 10 +++ conf/ovirt-agent | 12 ++++ conf/ovirt-db-omatic | 12 ++++ conf/ovirt-host-browser | 12 ++++