similar to: log transformation and mean question

Hello all, I am using 'plot' to create standard curves for elisa data. when I use 'plot' with type='b' i get the points connected with lines and one straigth line from the lowest datapoint to the highest data point. how can i avoid/remove it from the figure. i am using R2.9.1, below is the example of the data. od<-c(10, 8, 6,4,2,1, 10.5,7.8,6.4,3.8,2.1,0.95)

Hello, I am performing a meta-analysis using the metafor package. My data are proportions and I used the Freeman Tukey double arcine (FT) transformation to fit the random effects model. Now I want to create a forest plot with my estimates backtransformed to the original scale of proportions. Can this be done? Regards, Patricia

Hello gurus, I have a dataframe containing two groups viz., 'control' and 'case', each of these groups contains longitudinal data for 100 subjects. I have to plot all these subjects on a single chart and then put a regression line for each of the group for all the subjects. I have written a function to do the chart grpcharts<-function (dat, group,group2,molecule,cutoff){

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

At the risk of being beaten about the face and body, can somebody explain why the middle example: log2(2^3); floor(log2(2^3)) is different than examples 1 and 3? > log2(2^2); floor(log2(2^2)) [1] 2 [1] 2 > log2(2^3); floor(log2(2^3)) [1] 3 [1] 2 > log2(2^4); floor(log2(2^4)) [1] 4 [1] 4 > DrC [[alternative HTML version deleted]]

I figured out something new that I would like to see if I can do this more easy with R then Excel. I have these huge files with data. For example: DataFile.csv ID Name log2 1 Fantasy 5.651 2 New 7.60518 3 Finding 8.9532 4 Looeka -0.248652 5 Vani 0.3548 With like header1: ID, header 2: Name, header 3: log2 Now I need to get the $ID out who have a &log2 value higher then 7. I

Hi list, Can somebody explain why there are these warning messages?? I just don't get it.? I'm using R 2.15.1 on WinXP. Thanks! Tao > x [1] -2.143510 -1.157450 -1.315581? 1.033562 -1.225440 -1.179909 >? ifelse(x>0, log2(x), -log2(-x)) [1] -1.099975 -0.210950 -0.395700? 0.047625 -0.293300 -0.238675 Warning messages: 1: In ifelse(x > 0, log2(x), -log2(-x)) : NaNs produced

Hello. My name is Akashah. i work at metabolic laboratory. From my study, i found that volcano plot can help a lot in my section.  i already studied about the volcano plot and get the coding to run in R software, unfortunately, there is may be something wrong with the coding. This is because  no graph appear, but no error (blue color text) was shown on the R console. Below is the coding for

HELLO, anybody... could you help me to check the below coding for volcano. what is the mistake? what the plot could not display? # volcano_plot.r # # Author: Amsha Nahid, Jairus Bowne, Gerard Murray # Purpose: Produces a volcano plot # # Input: Data matrix as specified in Data-matrix-format.pdf # Output: Plots log2(fold change) vs log10(t-test P-value) # #

Dear list, I have a data frame like: > log2.ratios[1:3,1:4] Clone a1 a2 a3 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 how to make it to look like: > log2.ratios[1:3,1:4] a1 a2

I have some question about metafor package. I'm interest to perform a random effect meta-analysis of proportion (single group summary of prevalence of disease in a population as reported by different study) It ask: 1. "PFT": The Freeman-Tukey double arcsine transformed proportion is reported to be equal to 1/2*(asin(sqrt(xi/(ni+1))) + asin(sqrt((xi+1)/(ni+1)))). Hovewer, i

This is very minor, but shouldn't log2(quote(1:10)) throw an error,the same as log() and other math functions do? It looks like log2 and log10 evaluate a call object instead of throwing a non-numeric-argument error. They do object to non-call language objects, like expressions. > log2(quote(1:10)) [1] 0.000000 1.000000 1.584963 2.000000 2.321928 2.584963 [7] 2.807355 3.000000

I submitted a series of patches to convert all uses of log2 values to non-log2 values (That was harder than I thought because the types of the two are the same. They only different in meaning. So it was not easy to distinguish them. I split up patches so that anyone can verify correctness of the conversion that I've done.) >From now on, please always use non-log2 alignment values

Full_Name: Allan McRae Version: 1.6.0 OS: Win 2000 P Submission from: (NULL) (129.215.190.229) When using predict.Arima in library ts(), it appears differencing is only accounted for in the first step of prediction and so any trend is not apparent in the predictions. The example shows the difference between the predictions of an arima(1,1,1) model and the backtransformed predictions of an

Hello, I am trying to fit my Elisa results (absorbance readings) to a standard curve. To create the standard curve model, I performed a 4-parameter logistic fit using the 'drc' package (ExpectedConc~Absorbance). This gave me the following: > FourP A 'drc' model. Call: drm(formula = Response ~ Expected, data = SC, fct = LL.4()) Coefficients: b:(Intercept) c:(Intercept)

Hello I'm trying to write a function to calculate the relative entropy between two distributions. The data I have is in table format, for example: > t1 <- prop.table(table(c(0,0,2,4,4))) > t2 <- prop.table(table(c(0,2,2,2,3))) > t1 0 2 4 0.4 0.2 0.4 > t2 0 2 3 0.2 0.6 0.2 The relative entropy is given by H[P||Q] = sum(p * log2(p/q)) with the

I have a text file log2.log encoded Ansi in Windows. When I execute: out <- read.zoo(readLines(con <- file("log2.log", encoding="UCS-2LE")),FUN = as.chron) have errors: Error en file(file, "rt") : no se puede abrir la conexi?n Adem?s: Mensajes de aviso perdidos 1: In file(file, "rt") : s?lo fue usado el primer elemento del argumento

I'm looking over good-code a post-doc in my lab wrote and trying to learn how it works. I came across the following: rel.abundance <- as.matrix(read.delim("rel.abundance.csv",row.names=1,as.is =TRUE)) rel.abundance <- log2(rel.abundance-min(rel.abundance)+1) I'm not sure what the second line is doing. I ran each line in R and couldn't see a noticeable difference in

Hi Guys , Now I try the script using the full path of the programs (/usr/bin , /usr/sbin ecc..) and all is running. Now I have a little problem: If I insert in the on connect or disconnect tag this script /etc/icecast/bin/script.sh and the script is this #!/bin/bash /bin/echo $1 > /etc/icecast/log/1.txt /bin/echo $1 > /etc/icecast/log/log2.txt Only the first line is going , the

Hello R guru's I am a newbie to R, In my research work I usually generate a lot of ELISA data in form of absorbance values. I ususally use Excel to calculate the concentrations of unknown, but it is too tedious and manual especially when I have 100's of files to process. I would appreciate some help in creating a R script to do this with minimal manual input. s A1-G1 and A2-G2 are