similar to: anyone using LARS package in R

Dear useR's I have a small basic problem which I am hoping to get some help with. I have a data frame, testSeq_df, with 1 row and 500 columns. Each column is a character (a,c,g or t). I want this sequence to have 4 factors (a,c,g,t). When I try the following: for(i in 1:500){ if (length(levels(testSeq_df[,i]))==1) levels(testSeq_df[,i]) <-

Hi All, I am trying to use the "Kernlab" package for training and prediction using SVM's. I am getting the following error when I am trying to use the predict function: > predictSvm = predict(modelforSVM, testSeq); Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") : contrasts can be applied only to factors with 2 or more levels The training file is a

Hi All, Did anyone else have a problem like this? I am sorry if its a small issue, I seem to not understand what to do to get rid of this error. > Sigma [1] 0.1939025 > MuRest [1] 8.512772 > TauZero [1] 0.1 > curve(qlnorm(x,-TauZero+MuRest, Sigma,lower.tail=F), xlim=c(4000,9000), ylim=c(0,.99),xlab="", ylab="") Warning message: In qlnorm(p, meanlog, sdlog,

Hi useR's, I am resending this request since I got no response for my last post and I am new to the list so pardon me if I am violating the protocol. I am trying to use the "Kernlab" package for training and prediction using SVM's. I am getting the following error when I am trying to use the predict function: > predictSvm = predict(modelforSVM, testSeq); Error in

Hi, I am writing to seek some guidance regarding using Lasso regression with the R package LARS. I have introductory statistics background but I am trying to learn more. Right now I am trying to duplicate the results in a paper for shRNA prediction "An accurate and interpretable model for siRNA efficacy prediction, Jean-Philippe Vert et. al, Bioinformatics" for a Bioinformatics project

Hi All, This is more of a general statistics question that I am not so sure about so I need some thoughts from you experts out there. I have Chip-Seq read count data for 2 different treatments (T1 and T2) and my final aim is to calculate differential expression between them. I also have Chip-Seq read count data from a "control / wild type (C)" experiment. I have 3 replicates (2

Hi, I apologize for posting this here, I am also trying to post this on machine learning emailing lists. I have a set (18K) of sequences (22 nt long) and I have their counts at 4 different stages. The difference in counts from one stage to the next represents how well the sequence performed in the transition. The total counts remain about the same in each stage. So if a 1 sequence loses some

Hi there! I'm having some strange permissions issues with one of my systems that's on an Active Directory domain. Here's the basic background: - System is joined to AD domain. Users authenticate fine via Kerberos, and are authorized via an AD user group. They can browse the share, create files, etc. without incident. "valid users" lets them in. - User information for the

Gabor, Thanks much. Your solution is elegant. My overall scheme is to take present date, and check whether it is a weekend, if not, then create a string based on the date, to concatenate into a url link for download.file( ). The files I need to download have a part which is in the format: mmddyy. I am working to make myself a system to connect to exchanges, and download end of day files from

Hello, In a way similar to speexclient voip example, I want to have a voip application where 3 or more users can interact. This creates the following problems "1. How to playback 2 or more audio streams such that they appear overlayed (parallel)". The audio streams are speex encoded. I have few approaches in mind. 1. Create multiple decoder states and multiple ALSA audio playback

I have a dataframe say: date price_g price_s 0.34 0.56 0.36 0.76 . . . . . . and so on. say, 1000 rows. Is it possible to add two columns to this dataframe, by computing say diff(log(price_g) and diff(log(price_s)) ? The elements in the first row of these columns cannot be computed, but

date <- as.POSIXlt(Sys.time()) #present date for (i in 1:difftime(as.POSIXlt(Sys.Date()),"2007-10-01")) if (date$wday != 0 & date$wday != 6) {print(date);assign("date", (date-86400))} else (assign("date", (date-86400))) I am trying to print dates from present day to a day in the past, but omitting weekends. I am not doing something right, but can't

Hi Matt, All, Thanks for looking into this and your suggestions. I compiled the program with -O3 optimization level (clang -O3) on X86_64 target. After your suggestion, i ran the program with iteration of 10000 runs and found that average runtimes are (attaching data collected as well) Forward loop traverse : 2.006 milli seconds Reverse loop traverse : 1.531 milli seconds Yes, i agree that

Hi, I was working on multithreading a cross iteration loop. I want to insert a pthread_create function call and use other pthread functions into my LLVM IR. Issue is how do i get these functions using module->getOrInsertFunction("pthread_create"), since the function might not be there in IR and then insert function calls to these functions. So, crux is how do i call pthread

Can someone throw light on the following problem I am having with RODBC? There's an Excel file I am trying to read from, it has one sheet named 'nameclass'. Thanks in anticipation. Vishal Belsare > library(RODBC) > con = odbcConnectExcel(file.choose()) > tbls <- sqlTables(con) > tbls TABLE_CAT TABLE_SCHEM TABLE_NAME TABLE_TYPE REMARKS 1

Is there any existing implementation in R/S of : 1] Pincus & Kalman's approximate entropy (ApEn) measure 2] Total Correlation / Multiinformation 3] Information Interaction A search doesn't quite reveal anything, but I'd be keen to not reinvent in case someone has worked on it. Many thanks in anticipation. Best, Vishal Belsare

Hi, I am very very new to both Ruby and Ruby on Rails. I have been given a task to create a web application, which is able to edit individual entries in a key-value file. In other works, I would need to create an application which can parse a key-value file. Could someone guide me where I should start in a case like that? I was able to access and edit database table entries using Rails, but I

I am trying to download a bunch of files from a server, for which I am using download.file( ) within a for loop. The script is working fine except until download.file hits a URL which has no file, at which point it exits. I want to change this behavior to simple log the failure and maintain state within the for loop and iterate to next. I read about try / tryCatch but am having trouble

Hi. Can anyone point me to any module in R which implements "Little's Chi Square test" for MCAR. The problem is that i have around 60 behavioural variables on a 6 point categorical scale which i need to test for MCAR and MAR. What i can make out from preliminary analysis is that moderate (0.30 to 0.60) correlations may be present in several variable pairs leading me to suspect

I have an ordered series of 3 month t-bill rates (annual). I transform this to a daily series, however, the observations are constructed only from the dates on which the t-bills were issued, which is every week. So now I have ordered observations of the daily 'risk-free rate' for one day every week. I want to expand this zoo object to give a value for every day, and to do so, copy the