[R] BINARY traits GENETIC CORRELATION

2013-06-20 Thread Vallejo, Roger
Dear R Users, I have always used ASReml, MTDFREML, SAS, etc. to estimate genetic correlation (Rg) between two continuous quantitative traits (also continuous and binary trait) but I have never used R package to estimate Rg. However, I use R package for many of my other statistical analysis needs

[R] BINARY traits GENETIC CORRELATION

2013-06-20 Thread Vallejo, Roger
Dear R Users, I have always used ASReml, MTDFREML, SAS, etc. to estimate genetic correlation (Rg) between two continuous quantitative traits (also continuous and binary trait) but never used R to estimate Rg. However, I use R for many of my other statistical analysis needs; the R package is a gr

[R] beadarray package

2009-06-30 Thread Vallejo, Roger
Dear R users, I am using the beadarray package. I am trying to upload raw bead-level data using these commands: library(beadarray) datadir <- ("C:/Computer_programs/R/beadarray/cecilia") targets = read.table("targets.txt", sep = "\t", he

[R] nlme package

2007-12-26 Thread Vallejo, Roger
In using the NLME package (R 2.6.1 for Windows), I am having a problem in running an R script that used to run with no problems using a Linux OS in 2004. So I am wondering if during these last ~3 yrs we had major changes in the syntax of the NLME package that I am not aware. This is the R scr

[R] Affy Package

2007-12-26 Thread Vallejo, Roger
Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdif

[R] Affy Package

2007-12-24 Thread Vallejo, Roger
Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdif