similar to: exonmap question: rma (or justplier) crashes

Hi, I am trying to install the package exonmap and RMySQL however I keep getting the following error: "Error in library(pkg, character.only = TRUE) : 'RMySQL' is not a valid package -- installed < 2.0.0?" I have R version 2.4.1 so I know its not a version issue. I deleted and reinstalled the folders again and the same thing happened. Has anyone any ideas? Thanks,

Hello, A newbie to R. I am trying to use the exonmap package in R. According to the docs, the xmapDatabase() command should read the config file with all the connection parameters and connect to the DB. But i get the error shown below.... > xmapDatabase("Human") Error in mysqlNewConnection(dbDriver(drv), ...) : RS-DBI driver: (could not connect cagadmin at mysql2.cag.chop.edu on

Hi, I'm regressing various body dimensions upon body mass using the 'lmodel2' function, as I'm keen to obtain both OLS and RMA slope values. I also wish to create a plot of the regressions, with the 95% confidence interval of both the slope and intercept. I know how to plot 95% ci bands of the OLS slope using lm with the 'predict' function and 'matlines'. Does

Can anybody explain why RMA has to have a default normalization method: quantile-quantile? Why don't leave the choices to users? If I just want to use RMA to do a background correction without normalization, how should I specify the ? in the normalize.method="?" ? Hairong [[alternative HTML version deleted]]

Hi, i was looking into the documentation for the rma() function in affy() package, and was trying to figure out how exactly the background normalization is done. I read all three papers cited in the rma() documentation, but the most detailed explanation i could find was in Irizary et al., 2003, where they state that they compute B(PM_{ijn}) = E[s_{ijn} | PM_{ijn}] where s_{ijn} is assumed to

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Dear R-experts! I am working on some meta-analysis using the metafor package. I would like to extract values of the confidence intervals of the effect sizes of the single studies from an rma object. Those values are printed out when plotting a forest plot using the forest function on the rma object, however I was not able to locate them. Many thanks for your help! Jokel [[alternative HTML

I think that you misunderstood me. As far as I know, RMA does three things: background correction, quantile normalization, and summary from probes to probesets. I want the probe values after background correction and quantile normalization but before the summary. On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote: > pm(data) > > b > > On Dec

For starters, let me say again how impressive R is, and how all of the effort that has gone into R shines through clearly. It is an amazing program, and I am frequently pleasantly surprised to find out how powerful and capable R is. Finding the interface to xgobi is the latest pleasant surprise. Are there functions in R for Major Axis and Reduced Major Axis regression? I have OBS-RESID graphs of

I run R 1.9.0 on windows 2000, and have the following libraries installed: affydata_1.3.1 affy_1.4.23 Biobase_1.4.10 DynDoc_1.3.14 gcrma_1.0.6 hgu133acdf_1.4.3 hgu95av2cdf_1.4.3 hgu95av2probe_1.0 matchprobes_1.0.7 moe430acdf_1.4.3 multcomp_0.4-6 mvtnorm_0.6-6 rae230acdf_1.4.3 reposTools_1.3.29 rgu34acdf_1.4.3 tkWidgets_1.5.1 widgetTools_1.2.7 1. The rma function (in affy library) always crashes.

Anyone have any luck RMAing a Sipura phone since the Cisco take over? Sipura only has support via email or fax to end users and I haven't gotten a response to either for over 2 months. Linksys Support will jump you through all their scripted hoops to resolve your problem (they hope if they speak with a thick enough accent and make repeat the same steps over and over again that you will just

Greetings all. I am facing serious problems running ZFS on a storage server assembled out of commodity hardware that is supposed to be Solaris compatible. Although I am quite familiar with Linux distros and other unices, I am new to Solaris so any suggestions are highly appreciated. First I tried SXDE 1/08 creating the following pool: -bash-3.2# zpool status -v tank pool: tank state:

Hi (R 2.13.1, OSX 10.6.8) I am trying to use predict.rma with continuous and categorical variables. The argument newmods in predict.rma seems to handle coviariates, but appears to falter on factors. While I realise that the coefficients for factors provide the answers, the goal is to eventually use predict.rma with ANCOVA type model with an interaction. Here is a self contained example

Hi *, is there a way to obtain some kind of p-value for a model fitted with RMA using the lmodel2 package? I know that p-values are discussed and criticized a lot and as you can image from my question I'm not very much of a statistican (only writing my bachelor thesis). As fare as I understood the confidence interval statistic correctly, a coefficient is regarded as statistically significant

Hi, for testing if the slope of experimental data differs from a given slope I'm using the function "test_regression_against_slope" (see below). I am now confronted with the problem that I have data which requires a modelII regression (also called reduced major axes regression (RMA) or geometric mean regression). For this I use the function "modelII" (see below). What

Dear R-experts, The forest.rma() function from the metafor package creates nice forest plots for presenting the results of a meta-analysis. These plots can be annotated for e.g. giving names to the columns. E.g. as in the documentation of the package: data(dat.bcg) ### meta-analysis of the log relative risks using a random-effects model res <- rma(ai=tpos, bi=tneg, ci=cpos, di=cneg,

Dear R community, I'm using the ,metafor'-package by Wolfgang Viechtbauer (Version: 0.5-5) to calculate random-effects meta-analyses using Correlations and Sample Sizes as the raw data. (By the way: Really a nice piece of work, Wolfgang! Thanks heaps.) I specified the "rma.uni' function so that it looks like this: MAergebnis<-rma.uni(ri=PosOutc, ni=N,

I have a raidz2 pool with one disk that seems to be going bad, several errors are noted in iostat. I have an RMA for the drive, however - no I am wondering how I proceed. I need to send the drive in and then they will send me one back. If I had the drive on hand, I could do a zpool replace. Do I do a zpool offline? zpool detach? Once I get the drive back and put it in the same drive bay..

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many