similar to: Calculating all possible ratios

Buenas tardes, desde Uruguay, quiero realizar una regresión logística,con la función GLM, pero ademas quiero designarle a las observaciones clusters. La idea es decirle al programa que las observaciones corresponden a diferentes clusters. Saludos! Sebastián. [[alternative HTML version deleted]]

Dear R-help, I have fitted a glm logistic function to dichotomous forced choices responses varying according to time interval between two stimulus. x values are time separation in miliseconds, and the y values are proportion responses for one of the stimulus. Now I am trying to extrapolate x values for the y value (proportion) at .25, .5, and .75. I have tried several predict parameters, and they

Dear All, probably a simple enough solution but don;t seem to be able to get my head around it...example based on a publicly available data set: mydata <- read.csv("https://stats.idre.ucla.edu/stat/data/binary.csv") mylogit <- glm(admit ~ gre + gpa + rank, data = mydata, family = "binomial") library(effects) plot(allEffects(mylogit) ? ?

Hi, I have been using 'read.table' regularly to read tab-delimited text files with data. No problem, until now. Now I have a file that appeared to have read fine, and the data inside looks correct (structure etc), except I only had 15000+ rows out of the expected 24000. Using 'readLines' instead, and breaking up the data by tabs, gives me the expected result. I do not

Hi Everyone, I need some simple help. Here are my codes ##########will give me 10000 probesets#################### data.sub = data.matrix[order(variableprobe,decreasing=TRUE),][1:10000,] dim(data.sub) data_output<-write.table(data.sub, file = "c://data_output.csv", sep = ",", col.names = NA) When i export to excel, it shows me this. This is just a short version. There

Hi Guys, I am having a real hard time trying to figure out for microarry. Here is my code One-Sample t-Test dim(data.sub) [1] 10000 140 ##there are 10000 probesets and 140 columns hist(data.sub) ## Histogram. Identify if the probesets are normal distributed q<-rnorm(10000) ##generate 10000 random, normal distributed values qqplot(data.sub,q)) ##Show the plot of the probeset

Hi, I am relatively new to R and Bioconductor and am trying to filter the topTable that I generated of differentially expressed genes from my normlized eset file comprised of ~ 40 HG-133A Affy microarrays . I would like to see if particular probesets are represented in this list. Alternatively I would like to generate a topTable of differentially expressed genes using only specified probesets

Gracias a todos por sus respuestas, perdón si no fui muy claro. Lo que intento replicar es un análisis realizado en Stata, tengo que hacer los mismos cálculos pero en el r. En Stata lo que se hizo fue: xi: logistic i.coord i.v11_sexo, vce (cluster red) *Vce (cluster clustvar) especifica que los errores estándar permiten la correlación intragrupo, relajando el requisito habitual de que las

Hello: I am trying to work with a couple of microarray data sets, using platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 1 minor 8.1 year 2003 month 11 day 21 language R In the shortcut for invoking R I have set

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

so here is the code I need help to fix the line for 'st' when it reaches maximum, that's where i am getting stuck. thanks Sharad set.seed(100) d=data.frame(x=rnorm(20)+5, x1=rnorm(20)+5, x2=rnorm(20)+5, x3=rnorm(20)+5, x4=rnorm(20)+5, x5=rnorm(20)+5, x6=rnorm(20)+5, x7=rnorm(20)+5, x8=rnorm(20)+5) r2=c() cinit=0 for (col in 1:9) { cinit=cinit+1 st=cinit+1

Dear R-helpers I have a question related to logistic GAM models. Consider the following example: # Load package library(mgcv) # Simulation of dataset n <- 1000 set.seed(0) age <- rnorm(n, 50, 10) blood.pressure <- rnorm(n, 120, 15) cholesterol <- rnorm(n, 200, 25) sex <- factor(sample(c('female','male'), n,TRUE)) L <-

hello, Our database is in is-8859-1, and I want to update some text fields without success due to some accentuate characters ?? ect ... In my html page (where the charset is iso-8859-19) my textarea display the accentuate characters well and when the user post the form ... I thought that I just need to save it .... without success since ruby map one byte for one character ... So I

Dear all, I would like to know how to subset a data.frame by rows. Example: Probesets 34884 34888 34892 1 100009676_at A A A 2 10001_at P P P 3 10002_at A A A 4 10003_at A A

Dear R users, I want to aggregate all *d *data from all combination of n *plots* taken by k. Thank very much! My data is like that: plot d 1 14 1 13 1 12 1 14 1 18 1 20 1 21 1 43 1 108 1 43 2 41 2 61 2 83 2 61 2 84 2 45 2 21 2 12 2 11 ... 100 10 100 12 -- --- Catalin-Constantin ROIBU Forestry engineer, PhD Forestry Faculty of Suceava

***********reading in data********** data<-read.table("microarray.txt",header=T, sep="\t") head(data) dim(data) attach(data) ***********creating matrix and calculating variance across probesets******** x<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y]) variableprobe<-apply(data.matrix[x,],1,var) hist(variableprobe) **************filter out low

Hi everyone! I have a data frame with 1112 time series and I am going to randomly sampling r samples for z times to compose different portfolio size(r securities portfolio). As for r=2 and z=10000,that's: z=10000 A=seq(1:1112) x1=sample(A,z,replace =TRUE) x2=sample(A,z,replace =TRUE) M=cbind(x1,x2) # combination of 2 series Because in a portfolio with x1[i]=x2[i],(i=1,2,...,10000) means a 1

Here is my R Code x<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y])#create data.matrix variableprobe<-apply(data.matrix[x,],1,var) variableprobe #output variance across probesets hist(variableprobe) #displaying histogram of variableprobe write.table(cbind(data[1], Variance=apply(data[,y],1,var)),file='c://variance.csv') #export as a .csv file. Output in Excel all in 1

 Hi R-listers, Savings regression results after a loop is straightforward. But what about when you have nested loops? I am running a regression of the form  lm(y~1+x+M+ D[,i] + D[,j] + D[,k]) where x is the variable of interest. M and D are vectors with other covariates. Vectors "M" and "x" are included in every regression. Then i loop over the columns of D to use all

I am in need of someone's help in correlating gene expression. I'm somewhat new to R, and can't seem to find anyone local to help me with what I think is a simple problem. I need to obtain pearson and spearman correlation coefficients, and corresponding p-values for all of the genes in my dataset that correlate to one specific gene of interest. I'm working with mouse Affymetrix