similar to: CLUSTER 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-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

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 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,

In using the NLME package (R 2.6.1 for Windows), I am having a problem in running an R script that used to run with no problems using a Linux OS in 2004. So I am wondering if during these last ~3 yrs we had major changes in the syntax of the NLME package that I am not aware. This is the R script: library(nlme) treat=as.factor(c(1,2,1,2,1,2,1,2)) mouse=as.factor(c(1,1,2,2,3,3,4,4))

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 <-

I am running Xen on Debian wheezy. I switched from routed networking to bridged networking. Now I can''t seem to get eth0 to come up. When the network script tries to bring it up, it gets an error: RTNETLINK answers: File exists Any tips? details below brian root@trout:/etc/xen# egrep -v ''#|^ *$'' xend-config.sxp (network-script network-bridge) (vif-script vif-bridge)

I have a script that is attempting to notify a user that a job has finished. However, when called from within the script nothing is received by the user. When the equivalent message is sent from the command line, the user receives the message. The portion of the script that is relevant is below: ----- cut from script ----- #!/usr/bin/sh : : MESSAGE="$WINNAME, your job $_3GJOB\nhas

"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

I am designing an application to run a fishing tournament I am hosting. Each fish entered will be given a point total based on the length of the fish and the species of fish. Each species has a point multiplier. For Example Trout have a multiplier of 10 so a 20 inch Trout would have a score of 200. My conundrum is in where and when do I calculate the points. The options I have come up

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 have been getting quite a bit of PRI Resets using my Quad PRI Digium card. Prior to the resets I am getting similar notices to the following chan_zap.c:7482 pri_dchannel: PRI got event: HDLC Bad FCS (8) on Primary D-channel of span 3 Telco claims the PRI's are fine on their end and that it is my unit. Is this timing? (google somewhat leads to this) I am running 1.08 asterisk zaptel

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

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

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

I am currently submitting final copies of graphics to a journal for publication and they are asking that the fonts used in the plots are times new roman and 10 pt. I set the font size when I call the graphics device and in the par statement to 10. However, when I create a plot, the tick labels and axis labels are not 10 pts. I know I can use the cex commands to scale the fonts, but is there a

I am examining the following nlme model. asymporig<-function(x,th1,th2)th1*(1-exp(-exp(th2)*x)) mod1<-nlme(fa20~(ah*habdiv+ad*log(d)+ads*ds+ads2*ds2+at*trout)+asymporig(da.p,th1,th2), fixed=ah+ad+ads+ads2+at+th1+th2~1, random=th1+th2~1, start=c(ah=.9124,ad=.9252,ads=.5,ads2=-.1,at=-1,th1=2.842,th2=-6.917), data=pca1.grouped) However, the two random effects (th1 and th2)

Hello everyone. I would like to know if there is any R library to perform adaptive rejection sampling. Thanks in advance. ******************************************* Antonio Paredes USDA- Center for Veterinary Biologics Biometrics Unit 510 South 17th Street, Suite 104 Ames, IA 50010 (515) 232-5785 [[alternative HTML version deleted]]