similar to: Genotype importing from Sequenom

I have seen *some* similar activity in different machines through the years and it *always* turns out to be a hardware issue. If this machine is particularly old, I would be suspicious of that. Linc Fessenden ________________________________________ From: CentOS [centos-bounces at centos.org] on behalf of m.roth at 5-cent.us [m.roth at 5-cent.us] Sent: Wednesday, December 07, 2016 1:51 PM To:

Full_Name: Michael Aaron Karsh Version: 2.8.0 OS: Windows XP Submission from: (NULL) (75.61.102.255) Whenever I try changing a function, it keeps coming up with the same error message. I have the function CN_state_log_sum=function(Tot_log_sum){ #estimate copy number state for the log sum approach if(((Im(Tot_log_sum))!=0)|Re(Tot_log_sum)<=log(1/4)/log(2)) {return(0)}

Hi All, I have a problem trying to get a set of columns recognised as a list and can't work out how to do it despite trawling through the mailing list archives, and docs. A short example... to.convert <- NULL n <- 6 for(x in 1:n){ to.convert <- paste(to.convert, paste((2 * x) -1, (2 * x), sep=":"), sep=",") } to.convert <- gsub("^,", "",

I evaluated the Bayes factor in the k=2 allele case with a "triangular" prior under the null as in the example in the help file: HWETriangBF2(nvec=c(88,10,2)) [1] 0.4580336 When I swap the n11 entry and n22 entry of nvec, I received totally different Bayes factor: > > HWETriangBF2(nvec=c(2,10,88)) [1] 5.710153 > In my understanding, defining the genotype frequency as

Dear R mailing list, I have a dataset with genotypes from trios and I would like to infer haplotypes for each mother, father and child. The package that I could find that can do this is tdthap. But when the mother is homozygous (e.g., 2/2) the haplotype is called as not possible to infer (0); I would prefer for it to call the genotype (2). From what I understand it is doing what I would like

I have been merrily using the genetics package and more specifically have been using the makeGenotypes and genotypes function. I check my accomplishments by going > class(g2) [1] "genotype" "factor" and likewise > class(g1) [1] "genotype" "factor" Yet when I execute a command such as allele count I get this > allele.count(g1) D I [1,]

Our smallest network of systems has only four computers connected via Gigabit Ethernet.? The oldest and most stable platform is an eight year old Dell E520 running CentOS 6.8.? We often try out applications on this Dell/CentOS machine before moving them to other systems on our other networks. Last night, one of our users decided to create a single, 228GB home directory tar archive on an empty,

Hello, I'm having some trouble figuring out the correct model specification for my data. The system consists of multiple populations of an organism, which have been genetically sampled for several years. The problem is this: A minority of individuals are found in more than one sample, either they have survived into the next sampling at the same location, or have migrated to another another

R-users, I'm seeking any suggestions on optimizing some code for speed. Here's the setup: the code below is part of a larger chunk that is calculating Fst values across loci and alleles. This chunk is designed to calculate the proportion ('p.a') of an allele ('a') at a locus in each population ('p') and the proportion of individuals heterozygous for that

Matt Nelson <MNelson at sequenom.com> reported a problem using the Hmisc library that did not occur with versions of R before 1.6. I am running platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 1 minor 6.0 year 2002 month 10 day 01 language R > library(Hmisc) > g <-

Sorry for the off-topic question, but I know there are some talented LaTeX users out there. Which bibliography style gives only the year in text citations (e.g "for further details, see Anderson (1992)" )? Thanks Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 jasont at indigoindustrial.co.nz

Dear experts, For the makeGenotype function I need a list as in the example. However, since my list needs to be 184 long there must be an easy way to make it. >list(1:2,3:4,5:6,7:8) [[1]] [1] 1 2 [[2]] [1] 3 4 [[3]] [1] 5 6 [[4]] [1] 7 8 I have tried lis<-1:184 dim(lis)=c(92,2,1) as.list(lis) and several other options. Any suggestions? many thanks Marco [[alternative

Hello, I am using Mechanize to post a form to a website. When I do this by hand in my browser the response takes about 35s to come back (it''s a long page full of tables and graphics). When I do this with Mechanize, the server starts to respond and then appears to hang. The obvious conclusion is that my code is wrong but I am reasonably sure that I haven''t altered it

I have a vector with a long list of sentences that contain integers. I would like to extract the integers in a manner such that they are separate and manipulatable. for example: x[i] <- "sally has 20 dollars in her pocket and 3 marbles" x[i+1] <- "30 days ago john had a 400k house" all sentences are different and contain a mixture of both integers and characters. i

Hi, I have Agilent and Illumina SNP data. That's the only thing I know about the files - there seem to be no version specification in any of them. Is there a generic genotype calling algorithm that I could try to use on these datasets? thanks, N. -- View this message in context: http://www.nabble.com/generic-genotype-calling-algorithm--tp23141124p23141124.html Sent from the R help

Dear mailing list, I'm still quite a newbie in the statistical analysis of genotype/allele data, resp. more generally in the analysis of categorical variables. Moreover, I'm currently totally confused by the many R packages available to do such analysis. Here is my case: I've got a list of genes, and a number of case-control population pairs, and for each population and gene, the

Its really a matter of developing an intuitive method of interaction with t= he environment. Its very feasible and something that is easily realised. = The methods are tried and tested in games systems, 3D editors and even 3D f= ile managers. Thus, there are no new technical aspects, its merely the pac= kaging of those features into a desktop interface. =20 The business applications can be

Its really a matter of developing an intuitive method of interaction with t= he environment. Its very feasible and something that is easily realised. = The methods are tried and tested in games systems, 3D editors and even 3D f= ile managers. Thus, there are no new technical aspects, its merely the pac= kaging of those features into a desktop interface. =20 The business applications can be

Hi, I want to draw a scatter plot with 1M and more points and save it as pdf. This makes the pdf file large. So i tried to save the file first as png and than convert it to pdf. This looks OK if printed but if viewed e.g. with acrobat as document figure the quality is bad. Anyone knows a way to reduce the size but keep the quality? /E -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare

I use dChip and Affymetrix gtype to apply some genotyping functions to some microarrays data. Do you know if similar R functions exist? Thank you! Francesco ----------------------------------------------------------- Francesco Falciano, Ph.D. CINECA (High Performance Systems) via Magnanelli, 6/3 40033 Casalecchio di Reno (BO)-ITALY tel: +39-051-6171724 fax: +39-051-6132198 e-mail: