search for: pathogens

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

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

Dear R users & Experts, This is just a curiousity, I was wondering why the dominant eigenvetor and eigenvalue of the following matrix is given as the third. I guess this could complicate automatic selection procedures. 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 Please

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 3 ## 3

Dear all, I would like to know if it is possible to fit in R a Cox ph model with time-dependent covariates and to account for hierarchical effects at the same time. Additionally, I'd like also to know if it would be possible to perform any feature selection on this model fit. I have a data set that is composed by multiple marker measurements (and hundreds of covariates) at different time

Hello, I would like to know if there is a function in R that will test for normality and handle censored data sets. Currently, I evaluate each censored data set by the extent to which a normal scores plot approximate a straight line. For complete data sets I 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,

Hi The cor function in the stats package calculates the correlation between columns of data, does anyone know 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 -- --------------------------------

...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 m...

Dear All, Apologies for sending this email to both list, but at this point I'm not sure which one could help me the most. I have 4 sets of data, 1 test and 3 different sets of controls. The measurements are binary, 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

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 prof...

Hi, I would like some extra information on the 'cgh' package in R. I noticed that there isn't much activity regarding this package on the R and BioC mailing list (I googled it). I started using this package and I have few questions: 1/ As I have a custom tiling like array @8um features resolution (affy), I have a lot of probes to work with. I'm assuming it is correct to

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

Hi further to my upgrade question thanks for pointing me in the right direction any ideas how I get round the following problem: I'm trying to install on a Tru64 alpha ecs1h[jps]69: make `Makedeps' is up to date. `libappl.a' is up to date. `Makedeps' is up to date. `libnmath.a' is up to date. `Makedeps' is up to date. `libunix.a' is up to date. `Makedeps' is up

Hi All Not sure if this a bioconductor question or general R mailing list so apologies if this has gone to the wrong one................. When plotting dendrograms created by hclust you can "identify" clusters by clicking on the graphics and returning a list of what is contained in each cluster. However I'd like to be able to "zoom in" on specific clusters and plot

HI All sorry if this question has already been asked but I couldn't find anything that answered my question I have 24 columns of data that I'm trying to plot in heatmap.2 (gregmisc) and I'm having difficulty ordering them except in numerical sequence: I have transposed my matrix so it will appear with the dendrogram I want appearing at the top of the heatmap If I use either of

Hi I know this subject has been mentioned before but from the mail archives I'm under the impression that this is not possible ? I'm trying to carryout the equivalent of ls -l in R to give some date/time label to each of my objects If the case is that there is no equivalent, is it possible to list all objects in an environment that share a common component ? So that the common

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) > >...