similar to: wrong answer for simple expressions

cor.test and SuppDists give me different P-values for the same Spearman's rho. Which is correct, or am I doing something wrong? > x <- c(44.4, 45.9, 41.9, 53.3, 44.7, 44.1, 50.7, 45.2, 60.1) > y <- c( 2.6, 3.1, 2.5, 5.0, 3.6, 4.0, 5.2, 2.8, 3.8) > cor.test(x,y,method="spearman") Spearman's rank correlation rho data: x and y S = 48, p-value =

I have been unable to install the package RandomFields. I am using R 2.9.0-4 on Ubuntu 9.04. To install, I use the command: sudo R CMD INSTALL RandomFields_1.3.37.tar.gz The output follows below. Any help Would be appreciated. D. Hoysak Brandon University * Installing to library ?/usr/local/lib/R/site-library? * Installing *source* package ?RandomFields? ... ** libs g++

I have been unable to install the package RandomFields. I am using R 2.9.0-4 on Ubuntu 9.04. To install, I use the command: sudo R CMD INSTALL RandomFields_1.3.37.tar.gz The output follows below. Any help Would be appreciated. D. Hoysak Brandon University * Installing to library ?/usr/local/lib/R/site-library? * Installing *source* package ?RandomFields? ... ** libs g++

I am having difficulty with dependencies for the R rpm for Fedora Core 2. In attempting to load R-2.0.0.0.fdr.1.fc2.i386.rpm it fails the libtk8.4.so dependency even though I have this library loaded. The library is located in: /usr/local/lib. How might I tell R where to find this library? I am new to Linux and loading rpms so I am hoping there is a simple answer and that the problem is

Hello, I am trying to migrate an NT domain from an NT PDC to a samba3.0 PDC without disrupting users or requiring them to change passwords, etc. The complication is that there are NT fileservers in the domain already, so it's important that the users be transferred to the samba machine with SID's and RID's intact (so they can access these shares with the same permissions).

You asked the same question on the Bioconductor mailing list back in August. At that time, you suggested yourself a solution for how the adjusted p-values should be interpreted. I answered your query and told you that your interpretation was correct. So I'm not sure what more can be said, except that you should read the article Wright (1992), which is cited in the help entry for p.adjust(),

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

Hola a todos, Tengo un pequeño problemilla... Tengo unas 9000 variables que he contrastado con 1 en concreto con el test de wilcoxon. He calculado el p-valor, y queria corregirlo con el permutation-based FDR. He encontrado una funcion con R comp.fdr()que hace esta corrección, pero te pide que le pongas las variables con las observaciones y te hace el test (según he entendido). Yo solo quiero

Dear All, It is not a typical R question (though I use R for this) but I thought someone will help me. For the list of P values, I have calculated FDR using p.adjust() in R (bioconductor). But my FDR values are same for all the P values. When do we get same FDR values? Does the smallest P values should less than 1/N? (where N is the number of P values) Thanks in advance. Kind regards, Ezhil

I am getting the following error in my script. I am very very new to R and have obtained this script from another person. #read file in (dummy data) starburst.plot<-function(affy.fold, affy.FDR)(ifelse( ((affy.fold) >=0), -1*log10(affy.FDR), 1*log10(affy.FDR))) starburst.plot<-function(meth.fold, meth.FDR)(ifelse( ((meth.fold) >=0), -1*log10(meth.FDR), 1*log10(affy.FDR))) At my next

Dear List, We are planning a genotyping study to be analyzed using false discovery rates (FDRs) (See Storey and Tibshirani PNAS 2003; 100:9440-5). I am interested in learning if there is any consensus as to how many features (ie. how many P values) need to be studied before reasonably reliable FDRs can be derived. Does anyone know of a citation where this is discussed? Bill Dupont William D.

On Sat, 3 Jun 2017 16:04:57 -0700 Tim Northover <t.p.northover at gmail.com> wrote: [snip] > I think you should be able to fix it by changing the > compiler-rt/lib/xray/test/CMakeLists.txt. If you find the > "add_compiler_rt_test" call and move "-lstdc++" to the end, just after > "-lrt" it should work. Thanks, Tim. I don't see "-lrt":

I try to send this message To Gordon Smyth at smyth at vehi,edu.au but it bounced back, so here it is to r-help I am trying to use limma, just downloaded it from CRAN. I use R 2.0.1 on Win XP see the following: > library(RODBC) > chan1 <- odbcConnectExcel("D:/Data/mgc/Chips/Chips4.xls") > dd <- sqlFetch(chan1,"Raw") # all data 12000 > # > nzw <-

Hi, directory<- "/home/arunksa111/data.new" #first function filelist<-function(directory,number,list1){ setwd(directory) filelist1<-dir(directory) direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""), full.names = FALSE, recursive = TRUE) list1<-lapply(direct, function(x) read.table(x,header=TRUE, sep =

Dear R-people! I??m trying to write a C program that write to the standard input of R and read the standard output. I can perfectly read the R output, but I??m not able of writing anything to R. This program really works with the 'cat?? UNIX command, but it does not work with R. What I??m doing wrong??? It is possible to do it??? I want to start R once and use it thousands of times...

Dear R-people! I??m trying to write a C program that write to the standard input of R and read the standard output. I can perfectly read the R output, but I??m not able of writing anything to R. This program really works with the 'cat?? UNIX command, but it does not work with R. What I??m doing wrong??? It is possible to do it??? I want to start R once and use it thousands of times...

The Partek package (www.partek.com) allows only two selections for Multiple Test Correction: Bonferroni and Dunn-Sidak. Can anyone suggest why Partek implemented Dunn-Sidak and not the other methods that R has? Is there any particular advantage to the Dunn-Sidak method? R knows about these methods (in R 2.1.1): > p.adjust.methods [1] "holm" "hochberg" "hommel"

Hello, I do not understand the correct way to approach the following problem in R. I have observations of pairs of variables, v1, o1, v2, o2, etc, observed every 30 seconds. What I would like to do is compute the correlation matrix, but not for all my data, just for, say 5 minutes or 1 hour chunks. In sql, what I would say is select id, date_trunc('hour'::text, ts) as tshour,

On Tue, Aug 15, 2017 at 01:04:11PM +0000, Hatazaki, Takao wrote: > Ji-Hyeon, > > You're saying that "stripe=2 transport=rdma" should work. Ok, that > was firstly I wanted to know. I'll put together logs later this week. Note that "stripe" is not tested much and practically unmaintained. We do not advise you to use it. If you have large files that you

Hello, I've a question about the fdr method in p.adjust: What is the threshold of the FDR, and is it possible to change this threshold? As I understand the FDR (please correct) it adjusts the p-values so that for less than N% (say the cutoff is 25%) of the alternative hypothesis the Null is in fact true. thanks a lot for help, +regards, Arne