Displaying 20 results from an estimated 100 matches similar to: "problem with samr"
2011 Feb 09
1
samr - extract genes from siggenes.table
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,
2010 May 25
1
doubt about samr siggenes.table$genes.up
Hi, here's my siggenes.table$genes.up snippet.
Two class unpaired SAMR analysis.
"Row" "Gene ID" "Gene Name" "Score(d)" "Numerator(r)" "Denominator(s+s0)"
"Fold Change" "q-value(%)"
"1" "25" "RPL15P22" "RPL15P22" "-1.44115338424578" "-18"
2007 Aug 20
0
trouble extracting R code from vignette using example from www.bioconductor.org
Not sure if this is an R or BioC question so will cross-post. I cannot
extract R code from vignettes because system.file("doc",
"my.bioc.package") returns "". I got this code directly off of
http://www.bioconductor.org/docs/vignettes.html. A specific example
using siggenes follows but I have tested this using multiple packages,
including those for which I can
2023 Jul 04
0
[linux-next:master] BUILD REGRESSION 1c6f93977947dbba1fc4d250c4eb8a7d4cfdecf1
tree/branch: https://git.kernel.org/pub/scm/linux/kernel/git/next/linux-next.git master
branch HEAD: 1c6f93977947dbba1fc4d250c4eb8a7d4cfdecf1 Add linux-next specific files for 20230704
Error/Warning reports:
https://lore.kernel.org/oe-kbuild-all/202306260401.qZlYQpV2-lkp at intel.com
https://lore.kernel.org/oe-kbuild-all/202306301709.lvrxzyCj-lkp at intel.com
2006 Mar 10
1
need help in tune.nnet
Dear R people,
I want to use the tune.nnet function of e1071 package to tune nnet .
I am unable to understand the parameters of tune.nnet from the e1071 pdf
document.
I have performed nnet on a traindata and want to test it for class
prediction with a testdata.
I want to know the values of size,decay,range etc. parameters for which
the prediction of testdata is best.
Can anyone please tell me
2006 Jan 05
1
problem with command line arguments
Hello Everybody,
I am running a R script through a perl code from command line.
The perl script is like:
my $cmd= 'R CMD BATCH D:/try5.R';
system($cmd);
I run the perl code from command line.
Now I want to pass some command line arguments to the R script.
Its like the argv concept of perl.
Do I pass the arguments through my $cmd in the perl script?
If yes, then how to access that in
2004 Nov 22
1
Questions of Significance Analysis of Microarrays(SAM){siggenes}
Dear All:
Significance Analysis of Microarrays(SAM)
As we know sam do multiple t.test as following
## Default S3 method:
t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"),mu = 0,
paired = FALSE, var.equal = FALSE,conf.level = 0.95, ...)
var.equal: a logical variable indicating whether to treat the two variances
as being equal. If 'TRUE'
2007 Jan 23
3
the value of Delta
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
2006 Feb 02
0
problem with nnet
Hello All,
I am working with samr and nnet packages.
I am following the steps given below:
1> I take a input file with signal values for 9506 genes and 36 chips
, belonging to two classes.
2> I perform samr analysis on 80% of chip data from both the
classes.(selected by random sampling)
3> I then use the data of only the significant genes from this samr
analysis to train nnet.
4>
2006 Mar 23
0
front- end problem while using nnet and tune.nnet
Dear R people,
I am using tune.nnet from e1071 package to tune the parameters for nnet.
I am using the following syntax:
tuneclass <-c(rep(1,46),rep(2,15))
tunennet
<-tune.nnet(x=traindata,y=tuneclass,size=c(50,75,100),decay=c(0,0.005,0.010),MaxNWts
= 20000)
Here traindata is the training data that I want to tune for nnet which
is a matrix with 61 rows(samples) and 200
2010 Aug 24
0
SAMR for paired samples
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
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)
2005 Oct 07
0
Differentially expressed gene list
Hi,when I perform SAM on my array data(siggenes)I have some problems in
retrieving the separate lists of up regulated and down regulated genes.
When I write:
fold<-function(x){
gruppi<-split(x,controllo)
geni1<-abs(mean(gruppi[[2]])-mean(gruppi[[1]]))
return(geni1)
}
fold<-esApply(expr.contr.tratt.4,1,fold)
2006 Apr 27
0
pamr package: pamr.adaptthresh() error rates
Hi,
I was working on a classification problem using the pamr package. I used the pamr.adaptthresh() function to find the optimal accuracy of the classifier. I must not be doing it right, since it doesn't return the threshold values for optimum classification.
For example,if I run it on a dataset, I get the following result using pamr.adaptthresh():
predicted
true (1)
2006 Apr 27
0
package pamr: pamr.adapthresh() ---- Take 2!
Hi,
Sorry about the earlier formatting errors...
I was working on a classification problem using the pamr package. I used the pamr.adaptthresh() function to find the optimal accuracy of the classifier. I must not be doing it right, since it doesn't return the threshold values for optimum classification.
For example,if I run it on a dataset, I get the following result using
2006 Sep 14
0
Help On EBAM
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
2006 Sep 14
1
EBAM ERROR
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
2023 Aug 01
0
[linux-next:master] BUILD REGRESSION a734662572708cf062e974f659ae50c24fc1ad17
tree/branch: https://git.kernel.org/pub/scm/linux/kernel/git/next/linux-next.git master
branch HEAD: a734662572708cf062e974f659ae50c24fc1ad17 Add linux-next specific files for 20230801
Error/Warning reports:
https://lore.kernel.org/oe-kbuild-all/202307251531.p8ZLFTMZ-lkp at intel.com
https://lore.kernel.org/oe-kbuild-all/202308020154.Xrcb9bWT-lkp at intel.com
Error/Warning: (recently
2007 Nov 02
0
loading installes package including all needed subpackages
Hallo,
I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command?
Thanks, Corinna
Here is the result of the command library():
Pakete in Library
2008 Jun 10
1
samr result
Hello list!
I have a proble trying to perform a SAM analysis using the function samr
from the samr package. I have put the option *center.arrays=TRUE *in order
to scale all the experiments to median=0. I would like to retrieved the
scaled data but it seems that samr does not return it...Does anyone have any
idea on this?
Thanks a lot!!!
E.
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