similar to: Missing Data in Stepwise selection of Logistic regression

Hi All, I have a problem with weighted logistic regression. I have a number of SNPs and a case/control scenario, but not all genotypes are as "guaranteed" as others, so I am using weights to downsample the importance of individuals whose genotype has been heavily "inferred". My data is quite big, but with a dummy example: > status <- c(1,1,1,0,0) > SNPs <-

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other

Dear R User, Please, I am new to R. I want to overlay density plot for predictive interval pooled result in meta-analysis. http://addictedtor.free.fr/graphiques/graphcode.php?graph=114 Regards Frank Peter

Hello, I did a pca with over 200000 snps for 340 observations (ids). If I plot the eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot (rotation[,2]) I see a strange "column" in my data (see attachment). I suggest it is an artefact (but of what?). Suggestion: I used prcomp this way: prcomp (mat), where mat is a matrix with the column means already substracted followed by a

Hi all, rmvnorm()can be used to generate the random numbers from a multivariate normal distribution with specified means and covariance matrix, but i want to specify the correlation matrix instead of covariance matrix for the multivariate normal distribution. Does anybody know how to generate the random numbers from a multivariate normal distribution with specified correlation matrix? What about

I get the following error when I try reading in a table. How are 1.1, 1.2, 1.3 duplicate row names? Thx. > table <- read.table('latestWithNumber.txt', header=T) Error in "row.names<-.data.frame"(`*tmp*`, value = c("1.1", "1.2", "1.3", : duplicate 'row.names' are not allowed Yongchuan

I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? -- Thanks, Jim. [[alternative HTML version deleted]]

Hi all, I have a problem to estimate Std. Error and t-value by ?polr? in library Mass. They result from the summary of a polr object. I can obtain them working in the R environment with the following statements: temp <- polr(formula = formula1, data = data1) coeff <- summary(temp), but when the above statements are enclosed in a function, summary reports the following error:

Hi all, need help very urgently I did stepwise logistic regression for 35 covariates and added one SNP out of (500000) to get the best model for each model As my professor asked me using this command, outfiles <- paste(colnames(snps), ".txt", sep="") # list of output files for the best models for(i in 1:ncol(snps)) { model <- glm (Pheno~var1+var2+var3+..(all

Dear All, I am learning the ropes about logistic regression in R. I found some interesting examples http://bit.ly/Vq4GgX http://bit.ly/W9fUTg http://bit.ly/UfK73e but I am a bit lost. I have several questions. 1) For instance, what is the difference between glm.out = glm(response ~ poverty + gender, family=binomial(logit), data=mydata) and glm.out = glm(response ~ poverty * gender,

snpMatrix package is quite nice (read.plink())

 Hi, Is there any function available to do stepwise selection of variables in Conditional(matched) logistic regression( clogit)? step, stepwise  etc are failing in case of conditional logistic regression. Please help.  Thanks P.T. Subha [[alternative HTML version deleted]]

If I am buying a PC where the most compute intensive task will be running R and I do not have unlimited resources what trade-offs should I make? Specifically should I go for 1 - more memory, or 2 - faster processor, or 3 - something else? If it makes a difference I shall be running Windows on it and I am thinking about getting a portable which I understand makes upgrading more difficult. Extra

Hi, Anybody know what are the common Standard statistical methods used for the analysis of a dataset,and anybody know which of these methods give similar results Ram [[alternative HTML version deleted]]

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Hi, Is there any package for logistic model selection using BIC and Mallow's Cp statistic? If not, then kindly suggest me some ways to deal with these problems. Thanks. -- View this message in context: http://www.nabble.com/Stepwise-logistic-model-selection-using-Cp-and-BIC-criteria-tf4464430.html#a12729613 Sent from the R help mailing list archive at Nabble.com.

Dear R-help members, I'd like to run a binomial logistic stepwise regression with ten explanatory variables and as many interaction terms as R can handle. I'll come up with the right R command sooner or later, but my real question is whether and how the criterion for the evaluation of the different models can be set to be the probability of the residual deviance in the Chi-Square

I would like to perform a bootstrap validation of a backward stepwise logistic regression analysis, but I am a beginner with R and I am not sure of how to do it. Is there anyone that can send me a sample file in tab format (that I can modify in Excel by pasting my data) and the pertinent R algorithm? Many thanks Giuseppe -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dr. Giuseppe Biondi

I have been successfully been using R on my EEE PC for some while now. Although it uses Xandros I have been able to install various pieces of software by pretending that it was Debian etch. Johannes was kind enough to continue providing binaries on CRAN for a while but I think I am the only person still living in the past as CRAN etch is currently stuck at 2.11.0 and I cannot rely on him to

Dear R-experts, My problem is how to handle a 10GB data file containing genotype data. The file is in a particular format (Illumina final report) and needs to be altered and merged with phenotype data for further analysis. PERL seems to be an frequently used solution for this type of work, however I am inclined to think it should be doable with R. How do I open a text-file, line by line,