search for: logratio

...#39;s say the effect I'm looking at is response to two different kinds of drug treatment - let's call their effect sizes T1 and T2. Some studies have multiple experiments measuring T1 and T2. Some have one of each. Some only have T1 or T2. Now, in metafor, I've been using rma(yi = logRatio, vi=varLogRatio, mods=~ Drug.Type, data=mydata) This works fine. Out of curiosity, I ran a quickie model in lme4 lmer(logRatio ~ Drug.Type + (1+studyID), data=mydata, weights=varLogRatio) and I noticed that the results are quite different, and this appears due to some variation due to study (af...

I am using R to do a loess normalisation procedure. In 1.5.1 I used the following commands to normalise the variable "logratio", over a 2d surface (defined by coordinates x and y): > array <- read.table("121203B_QCnew.txt", header=T, sep="\t") > array$logs555<-log(array$s555)/log(2) > array$logs647<-log(array$s647)/log(2) > array$logratio<-array$logs555-array$logs647 > a...

I have got following error in drawing wavelet fitting. can some one help? > library(faraway) > data(lidar) > newlidar<-lidar[c(1:128),] > library(wavethresh) > wds <- wd(newlidar$logratio) > draw(wds) Error in plot.default(x = x, y = zwr, main = main, sub = sub, xlab = xlab, : formal argument "type" matched by multiple actual arguments [[alternative HTML version deleted]]

Dear R-users, I have an outcome variable and I'm unsure about how to treat it. Any advice? I have spending data for each county in the state of California (N=58). Each county has been allocated money to spend on any one of the following four categories: A, B, C, and D. Each county may spend the money in any way they see fit. This also means that the county need not spend all the money that

...ear mixed effects models. Maybe someone can give advise concerning the following problem: I have two groups of surgical patients in which repeated laboratory measurements were taken over time after surgery. I decided that lme would be the best model to fit the data. I already fitted the model lme(logratio ~ gr*I(pod-10) + I(pod^2-10) + I(pod^3-10), data=xyz, random = ~ pod|subj) where gr = two groups; pod = postoperative day; subj = patient; logratio = log of value at day pod/preoperative value: log(post/pre) but these questions remain: 1. Is lme the best model to fit the data? Other suggestions?...

HI everyone, I''m trying to assign colors to multiple lines in a graph. Problem is I don''t want to type in as many colors as there are lines....is there a way around this? In brief, I''m plotting the logratio for up to 60 samples and want a different color for each sample. Here is the code I''m using now.. Any help is greatly appreciated.. Best LT data <- read.table("data.csv", header=T, sep=",", stringsAsFactors= F) data$Pt <-as.numeric(data$Pt) npts <- unique...

...ot class directly? Here is an example explaing my question. Everything relates to S3/UseMethod classes and methods. I have an object x of class MicroarrayMatrix, which inherits from class Matrix. The "core" object of x is a simple matrix. In other words, I basically have x <- matrix(logratios, ncol=nbrOfSpots, nrow=nbrOfSlides) class(x) <- c("MicroarrayMatrix", "Matrix") Both these classes implement their own version of the "["() method. The "["() method of MicroarrayMatrix will return (spot, slide) values if called with two indices. Exampl...

...idx<-which(cnames=="GeneName") column.classes[idx]="character" idx<-which(cnames=="SystematicName") column.classes[idx]="character" idx<-which(cnames=="LogRatio") column.classes[idx]="numeric" idx<-which(cnames=="gMeanSignal") column.classes[idx]="numeric" idx<-which(cnames=="rMeanSignal") column.classes...

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...__gene_expression_analysis.txt", > header=T, row.names=1) in all cases I get the error "more columns than column names" I have only been able to read in the level II data with the code: > dat2<-read.table("C:\\US82800149_251976011000_S01_GE2_105_Dec08.txt_lmean.out.logratio.probe.tcga_level2.data.txt",header > = TRUE, as.is = TRUE, sep="\t") So this is what I am working with. I can see that the dimensions of this data are > dim(dat2) [1] 90798 2 When I print "dat2" to the screen it looks like this: I assume that this is one pati...

...mgcv package version1.7-22and R version 3.0.0 (2013-04-03) for fitting a GAM-Model to the LIDAR Data contained in the "SemiPar" package. Here is the code for fitting the model and for plotting the result: data("lidar") attach(lidar) ### # mgcv fitting ### gam_fit <- gam(logratio ~ s(range, k = 40, bs = "cr"), gamma = 1.4, method = "REML") plot(gam_fit, res = TRUE, shade = TRUE, pch = "°") Since the confidence interval in the above plot is pointwise, I would like to calculate the critical value needed in order to construct a simultaneous co...