similar to: samr-package: problem with large sample size multiclass data

Dear all, I'm looking for a method to quantify assortative mixing in undirected graphs, preferably something that is compatible with the igraph-library for network analysis. Is anybody aware of an already existing function/library for this or an easy way to implement this functionality in R? Many thanks, Rainer WikipediaWictionaryChambers (UK)Google imagesGoogle defineThe Free

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 =

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. [[alternative HTML version deleted]]

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

We have posted a major new version 2.0 of the samr package for large scale significance testing, especially for gene expression data. This new version handles RNA-seq data, using the new method described in http://www-stat.stanford.edu/~tibs/ftp/Li_Tibs.pdf We have also added simple interface functions SAM and SAMseq. Comments (and bug reports) welcome! -- I get so much email that I might

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)

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"

As far as I saw, since some microsoft patch for AD, winbind client from samba 3.0.14 (and prior versions) does not work properly for getting users and groups from Active Directory. This problem was solved in 3.0.20. I saw the following text in the samba 3.0.20 changelog: "Disable schannel on the LSA and SAMR pipes in winbindd client code to deal with Windows 2003 SP1 and Windows 2000 SP4

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,

Hello all, I'm working with the svm (libsvm) implementation from library(e1071). Currently I'm trying to extend recursive feature elimination (R-SMV) to work with multiclass classification. My problem is that if I run svm for a 3 class problem I get a 2-D vector back from model$coefs, can someone explain me what this values are? I understand them in the 2-class problem where this is a

Hi list, I'm toying with the idea of writing a m680x0 backend for LLVM, and the address modes of this chip are bewildering, to say the least. Here's a rough list off wikipedia for reference: * Register direct o data register, e.g. "D0" o address register, e.g. "A6" * Register indirect o Simple address, e.g. (A0) o

Is there a way to define a multi-class pattern in tablegen? Thanks, Micah Villmow Systems Engineer Advanced Technology & Performance Advanced Micro Devices Inc. S1-609 One AMD Place Sunnyvale, CA. 94085 P: 408-749-3966 -------------- next part -------------- An HTML attachment was scrubbed... URL:

On Mon, Feb 9, 2009 at 5:17 PM, Villmow, Micah <Micah.Villmow at amd.com> wrote: > Is there a way to define a multi-class pattern in tablegen? > Yes. See "multiclass" and "defm" in, say, X86Instr64bit.td, et al. -bw

In TableGen, can multiclasses inherit from one another? I notice that there's a lot of redundancy in the X86 .td files that could go away with multiclass inheritance. -Dave

On Mar 23, 2009, at 5:14 PM, David Greene wrote: > In TableGen, can multiclasses inherit from one another? I notice > that there's > a lot of redundancy in the X86 .td files that could go away with > multiclass > inheritance. Nope, not currently. That would be a nice feature though! -Chris

Hello, I just wanted to know if there's any package that implements error-correcting output code algorithms for multiclass ensemble problems. thank you in advance.

Hello all, this is the first time I'm using R and e1071 package and SVM multiclass (and I'm not a statistician)! I'm very confused, then. The goal is: I have a sentence with sunny; it will be classified as "yes" sentence; I have a sentence with cloud, it will be classified as "maybe"; I have a sentence with rainy il will be classified as "no". The

On Tue, Feb 10, 2009 at 8:27 AM, Villmow, Micah <Micah.Villmow at amd.com> wrote: > Bill, > Sorry if I wasn't clear enough. I wasn't referring to multiclass's that > define other classes, but with using patterns inside of a multiclass to > reduce redundant code. > For example: > multiclass IntSubtract<SDNode node> > { > def _i8 : Pat<(sub

Bill, Sorry if I wasn't clear enough. I wasn't referring to multiclass's that define other classes, but with using patterns inside of a multiclass to reduce redundant code. For example: multiclass IntSubtract<SDNode node> { def _i8 : Pat<(sub GPRI8:$src0, GPRI8:$src1), (ADD_i8 GPRI8:$src0, (NEGATE_i8 GPRI8:$src1))>; def _i32 : Pat<(sub

On 08/23/2017 11:35 AM, Jakob Stoklund Olesen wrote: > >> On Aug 22, 2017, at 14:15, Hal Finkel via llvm-dev >> <llvm-dev at lists.llvm.org <mailto:llvm-dev at lists.llvm.org>> wrote: >> >> For situations well beyond TableGen's current language capabilities, >> we have a decision to make. We can continue extending TableGen until >> it can