similar to: Error during wrapup: cannot open the connection

Hi BioC user, I have a problem extracting the gene set I would like to work with. Here is I work with my data: normData <- read.delim("normalizedData.txt",sep ="\t") ######### two class unpaired comparison # y must take values 1,2 classes <- c(-1,-2,1,2) #prepere the data for the samr analysis data.x <-as.matrix(normData[,8:11]) d=list(x=data.x,y=classes,

I'm running samr (Two class unpaired), but keep getting the following error: perm= 1 Error in if (logged2) { : argument is of length zero <code> library (impute) library (samr) data = list (x=dat, y=y, geneid = matrix(twoUnpaired.data[,1],ncol=1), genenames = matrix(twoUnpaired.data[,2], ncol=1)) samr.obj <- samr (data, resp.type="Two class unpaired", nperms=100)

Hello Everybody, I am trying to perform SAM with the samr package. I am using the following code: sink ("R005") library(siggenes) library(samr) library(nnet) A <- as.matrix(read.table("D:\samrgenes1000.txt")) B <- as.matrix(read.table("D:\genenames1000.txt")) y1 <- c(rep(1,20),rep(2,6)) #there are 20 chips of one kind and 6 of the other kind. datasam =

Hi, Can you please tell me what does the the function logged2 in R do im list or..? As I have > ?logged2 No documentation for 'logged2' in specified packages and libraries: you could try '??logged2' > ??logged2 No help files found with alias or concept or title matching ‘logged2’ using fuzzy matching. Thank you in advance, Amor [[alternative HTML version

Hi R-help, I am trying to use 'samr' for 10 pre and post paired samples to test whether post is different from pre (i.e., the location shift for the delta of (post-pre)). However, I got an error message saying > samr.obj<-samr(d, resp.type="Two class paired", nperms=100, random.seed=100) perm= 1 Error in !logged2 : invalid argument type Does anyone know what this

The entries in xenstore have permission attributes. The attributes can be easily altered by xenstore-chmod, however, I cannot find a easy way to see them. I''ve modified xenstore_client.c to raise a new utility. The utility checks the permission and makes an easy-look output. Please tell me any suggestions. Thanks. Signed-off-by: Frank Pan <frankpzh@gmail.com> ---

Dear R help; I'll preface this by saying that the example I've provided below is pretty long, turgid, and otherwise a deep dive into a series of functions I wrote for a simulation study. It is, however, reproducible and self-contained. I'm trying to do my first simulation study that's quite big, and so I'll say that the output of this simulation as I'd like it to be is

Hi, I am new to R. and even though I've made my code to run and do what it needs to . It is taking forever and I can't use it like this. I was wondering if you could help me find ways to fix the code to run faster. Here are my codes.. the data set is a bunch of 0s and 1s in a data.frame. What I am doing is this. I pick a column and make up a new column Y with values associated with that

Please forgive a stats question. I have to sets of data (unpaired) measured on an ordinal scale. I want to test to see if the two sets are different (i.e. do they have the same location): set1: 1,3,2,2,4,3,3,2,2 set: 4,4,4,3,3,5,4,4 What is the most appropriate non-parametric test to test location? Thanks, John Confidentiality Statement: This email message, including any attachments, is

Hi I have a vector x of length n. I am interested in x[1] being different from the other observations (ie x[-1]). My null hypothesis is that x[1] is drawn from a Gaussian distribution of the same mean as observations x[-1], which are assumed to be iid Gaussian. The (unknown) variance of x[1] is assumed to be the same as the variance of x[-1]. This should be an unpaired t-test. But

Dear RUsers, I am new to R. I am learning how to use R. I am a PC user and run R on windows. I would appreciate if some one could guide me on a few questions I have: 1) I have 4 cel files (2 replicates for NORM and Disease resp). I have been able to run siggenes on this dataset where I have 4 labels in the class file groupsnhi.cl op-> (0,0,1,1) and my data has been read into datrmanhi after

Hello, I''ve modified tools/xenstore/xenstore_client.c to include a new utility, xenstore-chmod. This utility permits developers and administrators to manually change the permissions on arbitrary locations in XenStore from the command line. This is often helpful if you''re trying to debug an application that relies on XenStore and is encountering difficulties with permissions.

Is there a way to override the queue wrapup time on the fly? I would like to allow a longer wrapup time for my agents, but if they are already done with closing up the call ticket, I would like them to be able to dial an extension or something to override the wrapup. Is there a way to do that? -- Regards, Robert Broyles

when subsetting a matrix results in a single row, it is converted to a vector, not a matrix. how do I avoid this? 1. __GOOD__ > edges <- get.edges(g,E(g)) > edges [,1] [,2] [1,] 0 2 [2,] 0 3 [3,] 0 4 [4,] 0 5 [5,] 1 1 [6,] 0 4 [7,] 0 6 [8,] 0 7 [9,] 0 8 [10,] 0 9 [11,] 0 5 [12,] 0 10 [13,] 0 11

Hi, I am using SAM (from siggenes_1.2.11 package) method to select genes from a microarray data set. After installing the latest R2.4.0 on my computer, to my surprise the results are totally different from that calculated using R2.1.1. Even the example code doesn't work the same way under these two versions of R. Does anybody know what is going on? Thanks for any suggestions.

Dear list, I am trying to perform a significance analysis of a microarray experiment with survival data using the {samr} package. I have a matrix containing my data which has 17816 rows corresponding to genes, and 286 columns corresponding to samples. The name of this matrix is data.matrix2. Some of the first values of this matrix are: data.matrix2[1:3,1:5] GSM36777 GSM36778 GSM36779

What this message means is that a "{" showed up when some other bracket was unpaired. In this case, if you check your code, you'll see that "if(MatriceDist[i,j] > 0 & ((vectorID[i] > 0 | vectorID[j] > 0))" is lacking a closing ")" for the if clause. Phalaen wrote > Hi! > I am a Phd student in the university of Padua and I am trying to

Dear all, I am running R 2.4.1. > library(siggenes); > library(multtest); > cl<-rep(c(0,1),c(3,3)); > sub<-exprs(AffyExpData[,c(1:3,7:9)]); > gn<-geneNames(AffyRAwData); > sam.out<-sam(sub,cl,rand=123,gene.names=gn); We're doing 20 complete permutations > sam.out SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances Delta p0

Hi all, I was wondering if there was a way to deal with "wrap up" time for agents slightly better than we do it at the moment. At the moment, we set a wrap up time of 20 seconds for each of our call queues. The problem with this is that sometimes it's either too long or two short. I would essentially like to have all agents put into wrap up straight after a call, and have to

Hi, I am not sure which kind of test is applied to the data if you use cor.test(x, y) ? Is it an unpaired t-Test? Regards -- View this message in context: http://www.nabble.com/cor.test%28x%2Cy%29-tp22492993p22492993.html Sent from the R help mailing list archive at Nabble.com.