[R] Multi-task SVM in R

Hi, Does anyone know of a package that implements Multi-task SVM in R? I found one in Matlab : http://www.ece.umn.edu/users/cherkass/predictive_learning/Resources/MTL_Software_Description.pdf I was wondering if there is something similar in R? Thank you for your help. Sincerely, Vishal

[R] Combining multiple dependent variables for machine learning

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 th

Re: [R] NAN problem

ylandt > > PS -- Thank you for providing a minimum working example and documentation > of your error messages. > > On Sat, Jul 30, 2011 at 4:04 PM, Vishal Thapar wrote: > >> Hi All, >> >> Did anyone else have a problem like this? I am sorry if its a small issue, &

[R] NAN problem

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),xl

[R] anyone using LARS package in R

this direction. Sincerely, Vishal -- *Vishal Thapar, Ph.D.* *Scientific informatics Analyst Cold Spring Harbor Lab Quick Bldg, Lowe Lab 1 Bungtown Road Cold Spring Harbor, NY - 11724* [[alternative HTML version deleted]] __ R-help@r-project.org mai

[R] seeking help on using LARS package

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 ef

[R] Statistics of count data for differential expression

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 r

Re: [R] Factor and Level Issue

Please ignore my message. I figured it out myself. The way to do it is: levels(testSeq_df[,i]) <- list(a=c('a'),c=c('c'),g=('g'),t=c('t')) Thanks, vishal [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.

[R] Factor and Level Issue

ues but still have 4 levels ie. a,c,g,t. Thanks a lot for your help, Vishal On Sat, Dec 26, 2009 at 10:39 AM, Vishal Thapar wrote: > Hi David, > > Thank you so much for the pointer. I get it now. I did try the > str(testSeq_df) and since it gave me more than 2 factors for each colu

Re: [R] Help with SVM package Kernlab

, 2009 at 8:26 AM, David Winsemius wrote: > > On Dec 26, 2009, at 3:53 AM, Vishal Thapar wrote: > > Hi All, >> >> Thank you for your replies so far. I was hoping I could get some more >> input from you on this issue. It seems to me that I have hit a dead end here >&

Re: [R] Help with SVM package Kernlab

Seq_seq,stringsAsFactors=FALSE) testSeq_df = cbind(Class="-",testSeq_df) testSeq_df = data.frame(lapply(testSeq_df,factor)) predict(mars500_1,testSeq_df) Error in .local(object, ...) : test vector does not match model ! Thanks in advance. Sincerely, Vishal On Fri, Dec 25, 2009 at 8:10 AM, V

Re: [R] Help with SVM package Kernlab

Hi, I seem to have made some headway on this problem but its still not solved. It seems like this is a "factor" issue. When I read my training set, I read it with read.csv() which converts each of the columns as "factors". From this if I take a single row as my testSeq, it works great. On the othe

Re: [R] Help with SVM package Kernlab

quot;, "V265", "V266", "V267", "V268", "V269", "V270", "V271", "V272", "V273", "V274", "V275", "V276", "V277", "V278", "V279", "V280", "V

Re: [R] Help with SVM package Kernlab

ss in the record removes the error. predictSvm1 <- (predict(modelforSVM, testSeq)); print(predictSvm1); chr4Seq = scan(my.file,list("",""),nlines=2); } Can't you just start with all of your data in a data.frame and "cut out" the > train

[R] Help with SVM package Kernlab

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 pred

[R] Error with Package "Kernlab" for SVM prediction

as well later to the testSeq data frame but got the same error. I am using R with windows, 32 bit, version 2.9.0 Any help is much appreciated. Thanks, Vishal -- Vishal Thapar, Ph.D. Post Doctoral Researcher Cold Spring Harbor Lab Williams Bldg 1 Bungtown Road Cold Spring Harbor, NY - 11724