search for: logged2

Displaying 6 results from an estimated 6 matches for "logged2".

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2009 Aug 12
1
logged2
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...
2010 May 24
1
Error during wrapup: cannot open the connection
...0] + u > y <- c(rep(1,10),rep(2,10)) > > data <- list ( x=x, y=y, geneid=as.character(1:nrow(x)), + genenames=paste("g",as.character(1:nrow(x))) ) > > samr.obj <- samr ( data, resp.type="Two class unpaired", + nperms=100, logged2=TRUE ) Error in samr(data, resp.type = "Two class unpaired", nperms = 100, logged2 = TRUE) : unused argument(s) (logged2 = TRUE) Error during wrapup: cannot open the connection > > > samr.obj <- samr ( data, resp.type="Two class unpaired", + nper...
2011 Feb 09
1
samr - extract genes from siggenes.table
...;,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, geneid=as.character(normData[,1]),genenames=as.character(normData[,1]), logged2=TRUE) samr.obj<-samr(d, resp.type="Two class paired", nperms=100) delta.table <- samr.compute.delta.table(samr.obj) delta=0.4 siggenes.table<-samr.compute.siggenes.table(samr.obj,delta, d, delta.table,min.foldchange=2) genes.up <- as.data.frame(siggenes.table$genes...
2005 Dec 26
0
problem with samr
...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 = list(x=A,y=y1,genenames=B,logged2=TRUE) testsamr <-samr(datasam,resp.type ="Two class unpaired",nperms=100) del <- 2 samr.plot(testsamr,delta) delta.table <- samr.compute.delta.table(testsamr) siggenes.table <-samr.compute.siggenes.table(testsamr,del,datasam,delta.table) sink() I am getting the following err...
2008 Jan 23
0
samr error
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) </cod...
2010 Aug 24
0
SAMR for paired samples
...amr' 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 means? or how to solve this error? Also, the options 'One Sample paired' is for testing the differences directly (d1, d2,...), I suppose. The source code is ***************************************** function() { library(samr) atta...