similar to: Linksys EFG20, RMA XH01210298

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

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

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 *, 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

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

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

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

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,

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,

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

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

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.

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

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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 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..

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:

I recently got a Pulver Innovations WiSIP wireless SIP phone to determine if we want to use them in our organization. Since the WiSIP phone arrived last week, I have had nothing but headaches. I do think I now have the problem narrowed down. I have spent a bulk of my time trying to get the WiSIP to work with a couple of Linksys WAP11 Version 2.2. I have met with no success in getting the WiSIP

Hello All, I need your help. I am analysing affymetrix data and have to select the probe-set that has median expression among all the probe-sets for same gene. This way I want to remove the redundancy by keeping the analysis to single gene entry level. I am fully aware that it is not a nice thing to do but I just have to do it. To do so, I came across 'findLargest' function of

Nevermind...need to read the whole msg... I didn't notice you were installing WINS on the NT box...hence the reboot. Standard practice for Winxx: 1. Install, reboot 2. Update, reboot, repeat.... I support about 25 pc's-it annoys the hell out of me how MS manages updates. How many Internet Explorer security updates have there been so far this year-22? Each one of them requires a