similar to: Need help with lmer model specification syntax for nested mixed model

Dear All, I am doing experiments in live plant tissue using a laser confocal microscope. The method is called "fluorescence recovery after photo-bleaching" (FRAP) and here follows a short summary: 1. Record/ measure fluorescence intensity in a defined, round region of interest (ROI, in this case a small spot) to determine the initial intensity value before the bleaching. This

Hello R-help I have the following data for a standard curve concentration(nM),fluorescence 0,48.34 2,58.69 5,70.83 10,94.73 20,190.8 50,436.0 100, 957.9   (1)Is there function in R to plot a spline. (2)How can I interpolation,say 1000 point from 0nM-100nM and store this as a data frame of concentration,fluorescence (3)How can I modify the code below so that instead of retrieving a concentration

Hi, I was wondering if I might be able to ask some advice about doing residual plots for the lmer function in the lme4 package. Our group's aim is to find if the expression staining of a particular gene in a sample (or "core") is related to the pathology of the core. To do this, we used the lmer function to perform a logistic mixed model below. I apologise in advance

Hello, Banging my head against a wall here ... can anyone light the way to a pattern modification that would make the following TRUE? identical( grep( "^Intensity\\s[^HL]", c("Intensity","Intensity L", "Intensity H", "Intensity Rep1")), as.integer(c(1,4))) Thank you for your time. Sincerely, Joh

Hi all, I have written a simple R script to help me analyze a large data set. I would like to have the script pause to allow the user to input a character string that is subsequently used as a filename when saving tables. I have tried to use the "readline" command - this seems to work fine when entering commands one by one, but when I copy and paste the entire script into R,

Hi again, Thanks Ted and Marc its works. But of course after pulling in in some real life data I discoverd one hitch. Often there are missing intervals. For example: from <- c(0, 1.2, 4.0, 4.2, 5.0, 25.0, 30.1, 45) to <- c(1.2, 4.0, 4.2, 5.0, 25, 30.1, 36.2, 50) intensity <- c(0, 1, 3, 2, 1, 0, 2, 5) barplot(intensity, width = -(to - from), space = 0, horiz = TRUE, ylim =

Hi everyone, I have a data frame that looks *sort of* like this: name <- letters[1:5] signal.1 <- c("12", "bad signal", "noise", "10", "X") length.signal.1 <- 5:9 intensity.signal.1 <- 3:7 signal.2 <- c("13", "noise", "19.2", "X", "V") length.signal.2 <- 2:6 intensity.signal.2

Hi I am attempting Anova analysis to compare results from four groups (Samp1-4) which are lists of intensities from the experiment. I am doing this by first creating a structured list of the data and then conducting the ANOVA (Script provided below). Im an R beginner so am not sure if I am using this correctly. Two major questions I have are: 1) Is using the code (zzz.aov <- aov(Intensity ~

Hi I needed some help with ANOVA I have a problem with My ANOVA analysis. I have a dataset with a known ANOVA p-value, however I can not seem to re-create it in R. I have created a list (zzzanova) which contains 1)Intensity Values 2)Group Number (6 Different Groups) 3)Sample Number (54 different samples) this is created by the script in Appendix 1 I then conduct ANOVA with the command >

Hello R users, I am working with the GAM to inspect the effect of some factors (year, area) and continuous variables (length, depth, latitude and longitude) on the intensity and prevalence of the common parasite Anisakis. I would like introduce interaction in my models, both "continuous variables-continuous variables" and "continuous variables-factor". I have read some

Hello, I have a question about how to plot a series of data. The folloqing is my data matrix of n > n 25p 5p 2.5p 0.5p 16B-E06.g 45379 4383 5123 45 16B-E06.g 45138 4028 6249 52 16B-E06.g 48457 4267 5470 54 16B-E06.g 47740 4676 6769 48 37B-B02.g 42860 6152 19276 72 35B-A02.g 48325 12863 38274 143 35B-A02.g 48410 12806 39013 175 35B-A02.g 48417 9057 40923

Sorry i had a misprint in the appendix code in the last email Hi I needed some help with ANOVA I have a problem with My ANOVA analysis. I have a dataset with a known ANOVA p-value, however I can not seem to re-create it in R. I have created a list (zzzanova) which contains 1)Intensity Values 2)Group Number (6 Different Groups) 3)Sample Number (54 different samples) this is created by the

Dear R-list, I would like to generate an intensity map based on a x * y matrix. Each point in the matrix should get plotted at the coordinate: x = column / y = row with a color-intensity (for example gray-value) based on the actual value of this point. Is there a convenient package / function for this kind of plot? example data: x <- matrix(rnorm(100*100, 0, 2), 100, 100) thanks!

Dear R-users. I'm struggeling to fix the superscript of a label of a figure axis. For some reason R doesn't recognize the "hat" symbol. plot(1,1,xlab="ligth intensity (PAR)",ylab=expression("mass Pteridium rhizomes" (gr/0.25m^2))) A very similiar scriptline does not give any problem at all: plot(1,1,xlab=expression("balsa plot basal

Hello, Can anybody help me understand the difference between the three different codes in specifying the slope in the random part of a mixed model using LMER? Here are the codes: (age | id) (1 + age | id) (age - 1 | id) Thank you in advance Arnaud

Dear all, I want to estimate a crossed-random-effects model (i.e., measurements, students, schools) where students migrate between schools over time. I'm interested in the fixed effects of "SES", "age" and their interaction on "read" (reading achievement) while accounting for the sample design. Based on a previous post, I'm specifying my model as: fm1 <-

Dear R-users, I'm using lattice package and function xyplot for the first time so you will excuse me for my inexperience. I'm facing quite a simple problem but I'm having troubles on how to solve it, I've read tons of old mails in the archives and looked at some slides from?Deepayan Sarkar but still can not get the point. This is the context. I've got data on 9 microRNAs, each

Dear all, Can anyone please shed some light onto how to do this? This will give me all "intensity" columsn in my data frame: intensityindeces <- grep("^Intensity",names(dataframe),value=TRUE) This will give me the maximum intensity for the first row: intensityone <- max(dataframe[1,intensityindeces]) What I'm now looking for is how to dfo this for the whole data

Hello, I am trying to download a SOFT matrix file for GSE series to extract raw intensity data. gse<- getGEO('GSExxxx', AnnotGPL=T) However, I am not able to use the function Table(gse), which returns the following error >>>Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Table", for signature "GSE" If I

Hello again, I am trying to create a color scale plotting the hydroathy index (y-axis) versus residue (x-axis) - each residue (1-100) has a value between 0-1. I've been trying to create a scale where: 0-0.499: increasing intensity of red 0.5- yellow 0.51 - 1 increasing intensity of green. THis is in lieu of a line graph. I'm not sure which type of plot to begin with - I attempted to