search for: pathogen

I am relatively new to R and am looking for advice, ideas or both... I have a data set that consists of pathogen population sizes on individual plant units in an experimental field plot. However, in order to estimate the pathogen population sizes I had to destroy the plant unit and could not determine if that plant unit became diseased or to what extent it would have become diseased. I collected disease...

Hi, First my apologies for a non-working piece of code in a previous submission, I have corrected this error. I'm doing is individual based modelling of a pathogen and it's host. The way I've thought of doing this is with two dataframes, one of the pathogen and it's genes and effector genes, and one of the host and it's resistance genes. During the simulation, these things can be pulled out of the dataframes and operated on, before being store...

...0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 Please copy & paste the following into R; a=c(0,0,0,0,0,5,1,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0) mat=matrix(a, ncol=6,byrow=T) eigen(mat) The matrix is a population matrix for a plant pathogen (Powell et al 2005). Basically I would really like to know why this happens so I will know if it can occur again. Thanks for any comments, Marco Visser Comment: In Matlab the the dominant eigenvetor and eigenvalue of the described matrix are given as the sixth. Again no idea why. reference...

Hi All, I'm trying to run a simulation of host-pathogen evolution based around individuals. What I need to have is a dataframe or table of some description - describing all the individuals of a pathogen population (so far I've implemented this as a matrix): ID No_of_Effectors Effectors (Sequences) [1,] 0001...

...is model fit. I have a data set that is composed by multiple marker measurements (and hundreds of covariates) at different time points from different tissue samples of different patients. Suppose that the data were coming from animal model with very few subjects (n=6) that were followed up given a pathogen exposure, measured several times, sampling different tissues in the same days, until a certain outcome was reached (or outcome censored). Suppose that the pathogen can vary over time (might be a bacteria that selects for drug-resistance) and that also it can vary across different tissue reservoirs...

...use shapiro.test(). Below is an example of a censored data set. data1<-c(0.00, 0.00, 0.00, 5.86, 5.17, 8.17, 5.12, 4.92, 7.08, 5.73, 5.44, 6.61, 6.34, 6.23, 5.97, 5.86, 5.15, 7.98, 6.72, 5.15, 3.58, 6.86, 6.12, 4.58, 6.07, 5.38, 5.21, 3.78) The zero values occur because I cannot detect a pathogen with a value below 2.4. Using shapiro.test(), it seems that the data are different from a normal distribution. However, the normal scores plot suggest otherwise. Using R version 1.9.1 Thanks in advance. Ken ________________________________________________________ Kenneth E. Frost Research A...

...if it is at all possible to calculate the correlation between rows instead ? Or is there an appropriate package or function that is more appropriate I'd like to calculate spearman & pearson correlations between rows. Many thanks Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

...S/PhD in computer science (or related field) with experience in bioinformatics. The Analytics Team is responsible for computational support for projects involving large chemical and microbial hazard data sets, including bioinformatic and statistical analysis of bacterial genomic data for foodborne pathogens. The individual works with a team of statisticians and bioinformaticians to develop and improve methods for detecting and identifying bacterial pathogens from food and environmental sources The successful applicant would be expected to effectively interact with various subject matter experts in...

...with a matrix of 0 and 1 I'm measuring across time (rows, ~815) the behaviour of organelles in the cell by microscopy in response to different stimuli (several measurements for each set, 57 columns in total) Set 1: parasite test Set 2: no stimulus Set 3: inert stimulus (beads) Set 4: different pathogen Across time, a "zero" means nothing happens around my parasite introduced in the cell, a "1" means some cytoskeleton dynamics occurring around my parasite I want to give some statistical value to my observations in saying that the cytoskeleton dynamics are specific to my parasit...

I am a relative newbie to survival analysis and R in general, but would like to use the coxme package to analyse some data I currently have. The data is relative to survival times of drosophila melanogaster populations to infection with pathogens, and has the variables: Time, Status, Treatment (4 treatments + 2 controls) Population Replicate ?and I'm currently using the following call mixed<- coxme(formula = Surv(Time, Status) ~ strata(Treatment) + (1 | Population/Replicate),x=T,y=T) The treatments have very different mortality pro...

...ats graphics grDevices utils datasets methods base other attached packages: [1] cgh_1.0-2 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 Thank you very much for your help, Best wishes celine ************************************** Celine Carret, PhD Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK tel.+44-1223494940 fax.+44-1223494919 ************************************** -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457...

Dear R users, I am sorry to disturb you! But I really need your help for the usage of sigPathwy. Actually, I want a sliding window analysis for possible chromosome expression pattern mining. My research microorganism is a plant pathogen, Gibberella zeae, and I first used SAS to divide locus number with 10, 20, 30, or 40 on the fungal chromosome according to their location. I really want to see whether among the continual 10, 20, 30, or 40 locus has some expression pattern that different from rest genes. Because I know sigPathway (...

...LIB Makeconf Makefrag.cxx RESOURCES aclocal.m4 config.status doc m4 tests COPYRIGHTS Makeconf.in Makefrag.f77 THANKS afm configure etc modules tools thanks J. -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

...atamat, DIF123clustFLIPasdendro, DIF123clustHCmcquittyasdendro, hclustfun=hclust) but this returns row dendrogram ordering gave index of wrong length which has come from the viseversa example above. thanks for any help and guidance Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

...quot;high", in some graphics functions but this isn't what I'm trying to do unless my data is evenly distributed i.e -60 to +60 I can't plot exactly how I want to If anyone has any ideas that would be fantastic Cheers Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

...xtract the object name & $ time from all objects simultaneously so I can compare them. Or am I just wasting my time ? Apologies but my knowledge of R is limited at best ;-( Any help would be fantastic and greatfully received Cheers Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

Hi, I've got an odd situation here. Somehow, I find myself with two files that start with the - character. [eric at apollo mysql]$ ls -l total 93348 -rw-r--r-- 1 mysql mysql 9273344 Nov 13 19:03 -N=2007-11-08 -rw-r--r-- 1 mysql mysql 38879232 Nov 13 19:02 --newer=2007-11-08 Don't ask how they were created; something went wrong with a script at some point. My problem is that I am

...: text/plain; charset=ISO-8859-1 > > I am a relative newbie to survival analysis and R in general, but > would like to use the coxme package to analyse some data I currently > have. > The data is relative to survival times of drosophila melanogaster > populations to infection with pathogens, and has the variables: > Time, > Status, > Treatment (4 treatments + 2 controls) > Population > Replicate > ?and I'm currently using the following call > mixed<- coxme(formula = Surv(Time, Status) ~ strata(Treatment) + (1 | > Population/Replicate),x=T,y=T) > >...