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