similar to: nlme package

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best

Dear R users, I am using the beadarray package. I am trying to upload raw bead-level data using these commands: ######################################################## library(beadarray) datadir <- ("C:/Computer_programs/R/beadarray/cecilia") targets = read.table("targets.txt", sep = "\t", header = TRUE, as.is = TRUE) BLData = readIllumina(arrayNames =NULL,

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.05 which is quite conservative (i.e., very

Hi Martin, In using the Cluster Package, I have results for PAM and DIANA clustering algorithms (below "part" and "hier" objects): part <- pam(trout, bestk) # PAM results hier <- diana(trout) # DIANA results GeneNames <- show(RG$genes) # Gene Names are in this object But

Dear All, How to cite the PDF user's guide for the LIMMA package? This is not about how to cite the LIMMA package. Roger Roger L. Vallejo, Ph.D. Computational Biologist & Geneticist U.S. Department of Agriculture, ARS National Center for Cool & Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Email: roger.vallejo@ars.usda.gov

Dear R-Help, I am using the LIMMA User's Guide 5 January 2007 PDF version. For the example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I could not grasp the rationale in developing the contrast.matrix with these R statements (">" indicates the R command prompt): > contrast.matrix <-

"Vallejo, Roger" <Roger.Vallejo at ARS.USDA.GOV> asked: > I would like to know if we can estimate Rg between two binary traits > (disease status: alive vs. dead) with the R package. > > My data: we have 100 full-sib (FS) families, > and two random samples (each with n= 200 FS fish) from each FS family > were evaluated for disease resistance to two different

Hello All, I am a R newbie and am probably misinterpreting something really obvious... In the Rcmdr package there is a scatter3d() function that can fit a curve and also provide coefficients for the model. If I'm understanding this right, I think it's calling the lower level stats package function lm(), which is the part that actually does the curve fitting. Anyway, what has me

I am running R and R64 on a MacBook Pro (2.66GHz, 8GB, OS X 10.6) and it keeps freezing up on me (i.e. have to force quit or kill). Same problem with both R and R64. I am not doing heavy computation, mostly just editing some scripts in the GUI. Also the computer is plenty fast with sufficient memory. I looked around but haven't seen anything on this problem. Thanks! -- Jesse

The USDA-Agricultural Research Service, Southeast Watershed Research Unit in Tifton, GA, is seeking a postdoctoral research associate for a full-time, 2 year appointment. The research associate will develop, calibrate, and validate a semi-empirical model for estimating cotton biomass from fields within the southeastern United States. Model development will involve the use of optical and radar

Hi, In R 3.4.0, the "Pattern Matching and Replacement" documentation that describes regexec(), gregexpr(), etc. states that the "text" argument to regexec is a character vector, "or an object which can be coerced by as.character to a character vector": regexec(pattern, text, ignore.case = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE)

Dear R-Help, Does anyone know of a way to use CGIwithR in Windows? David Firth the author of CGIwithR states "It ought to be possible to adapt it for use also in conjunction with web servers running under Windows NT ... but the author has no plans for that." I have developed some applications in R that I would like to make available through a web interface using CGIwithR but at this

Does R have something equivalent to the "goto" in Perl? If so, can you please tell me what it is? I cannot find it in the Ref Manual or the Language Manual. Thanks. - Warren Warren Lamboy USDA-ARS Plant Genetic Resources Unit Geneva, NY, USA 14456

If I have 3 columns of data, col 1 = Independent Var; cols 2 and 3 are Dep. Vars. I would like to produce a plot with both: col2=f(col1) and col3=f(col1). How do I do this such that I can control line parameters (line type, color, etc). I know that if I stack the data and col2 and col3 are treated as different factor levels, that I can accomplish this, but lose control over the line

I've taken my RH7.1 system, rebuild kernel (2.4.9 with ext3 patches) and followed the ext3 instructions to install. Everything seems to work OK but - df -k doesn't list the ext3 partition (my root partition). Is this a known problem ? If not, how best can I gather diagnostics to identify the source of the problem ? Thanks -- Philip Nelson (teamdba@bojnice.com)

Is there any way to put an argument into an object name. For example, say I have 5 objects, model1, model2, model3, model4 and model5. I would like to make a vector of the r.squares from each model by code such as this: rsq <- summary(model1)$r.squared for(i in 2:5){ rsq <- c(rsq, summary(model%i%)$r.squared) } So I assign the first value to rsq then cycle through models 2 through

Buenas tardes a tod@s, Estoy incursionando en el analisis de tweets utilizando el paquete twitteR y siguiendo http://www.webmining.cl/2012/07/text-mining-de-twitter-usando-r/ Desafortunadamente cuando ejecuto # cargar librerias library(twitteR) library(tm) library(wordcloud) # recolecta tweets de @camila_vallejo tweets = userTimeline("camila_vallejo", 2000) obtengo Error in

Como integrar asterisk con Ldap.?? Saludos -- Dario Javier Estupi?an Vallejo darioestupinan at soygenial.co Investigaci?n y Desarrollo - Neiva Corporaci?n Polit?cnica Nacional ................................................. -------------- next part -------------- An HTML attachment was scrubbed... URL:

Saludos, necesito saber la ubicaci?n del archivo con contrase?as por default para porder ocultarlo. Gracias. I need to know the addres or location of file with passwords for default thanks! -- Dario Javier Estupi?an Vallejo darioestupinan at soygenial.co Investigaci?n y Desarrollo - Neiva Corporaci?n Polit?cnica Nacional ................................................. -------------- next

Saludos, Como oculto una carpeta en asterisk sin da?ar la informaci?n ejemplo: cdr_mysql.conf gracias -- Dario Javier Estupi?an Vallejo darioestupinan at soygenial.co Investigaci?n y Desarrollo - Neiva Corporaci?n Polit?cnica Nacional ................................................. -------------- next part -------------- An HTML attachment was scrubbed... URL: