similar to: extracting pvalues from ttest

Hello all, I have arranged my data as per Dennis's suggestion in this post http://www.mail-archive.com/r-help at r-project.org/msg107156.html. the posted code works fine but when I try to apply it to my data, i get "> u2 <- ddply(xxm, .(plateid, cytokine), as.data.frame.function(f)) Error in t.test.formula(conc ~ Self_T1D, data = df, na.rm = T) : grouping factor must have

Hello R gurus, I have the code below for which i need help and pointers to make it run in parallel on a dual core win7 computer with R 2.13.x, using foreach, iterators,doMC. library(scatterplot3d) # Loads 3D library. library(fields) library(MASS) library(ROCR) library(verification) library(caret) library(gregmisc) ##simulated data d=replicate(9, rnorm(40)+10)

Hi everyone, I've just installed "rw1040" and all the components necessary to compile packages for windows. I always try out my new installation on the provided package "windlgs" in order to ensure that everything is working. This time I ran into a small problem. Indeed, the second line of "ttest.c" includes a header file ("ga.h") which does not

Hello, I would like to do a large number of e.g. 1000 paired ttest using the by-function. But instead of using only the data within the 1000 groups, R caclulates 1000 times the ttest for the full data set(The same happens with Wilcoxon test). However, the by-function works fine with the lme function. Did I just miss something or is it really not working? If not, is there any other possibility to

We are trying to compile and run the ttest.c example that comes with R (in C:\Program Files\R\rw1081\src\library\windlgs\src\ttest.c). After compiling it with MS Visual C++ we load the DLL with dyn.load. So far it seems good, but when we try to call it from R (after running C:\Program Files\R\rw1081\src\library\windlgs\R\windlgs.R) R crashes. We have tried changing the exports from DLL but have

Dear list, i am a biologist who needs to do some ttest between disease and non disease, sex, genotype and the serum levels of proteins on a large number of individuals. i have been using excel for a long time but it is very tedious and time consuming. i am posting the data below and ask your help in generating a code to get this analysis done in R. thanks gender disease genotype data M N CC

dear all- If I have a vector of numbers (not necessarily normally distributed) how can I get the p-value of a number in this distribution. I am interested in the "inverse" of 'quantile' . thank you- Maya

Hi all, I have some microarray data on 40 samples that fall into two groups. I have a value for 480k probes for each of those samples. I performed a t test (rowttests) on each row(giving the indices of the columns for each group) then used p.adjust() to adjust the pvalues for the number of tests performed. I then selected only the probes with adj-p.value<=0.05. I end up with roughly 2000

Hi, I have run a groups of t test and obtained a list of the t-test results (about 30). How do I extract p-values from the 30 t-test results and make a table output? Thanks Jun Example t-test output: ============================ $Lambda_z Welch Two Sample t-test data: x[PA1.BS.DN$Onecode == 2] and x[PA1.BS.DN$Onecode == 3] t = -0.1128, df = 33.635, p-value = 0.9109 alternative

Hello ... I've noticed that some of our Bioconductor code was running drastically slower under current R-devel vs. current R-patched - one example is below using a ttest. I have the following snippet of code that demonstrates the problem while avoiding "real" code that takes an extremely long time to finish on R-devel: library(genefilter) data(eset) eset$cov1 z <-

Hi, How do I generate bootstrap p-values for goodness of fit test. Thank you in advance for your help, Juliet [[alternative HTML version deleted]]

Dear R users, I have developed a model I have compared several options of obtaining p-values for poisson lmer model including Marlov chain monty carlo methods, single term deletions and summary. > > However, I encountered several problems that can be classified as > (1) the p values from the summary command are total different from those derived from Marlov chain monty carlo methods >

Hi All, I have run many regression analyses (14000 +) and want to collect the coefficients and pvalues into an excel file. I can get the statements below to work up to step 4. I can printout the regressionresults (sample output below). So my hope is to run something like step 5 and 6 and put the pvalues (and then coefficients) into an excel file. Can anyone suggest what I am doing wrong or a

Hi all, My data genes [,1] [,2] [,3] [,4] [1,] 25 72 23 55 [2,] 34 53 41 33 [3,] 26 43 26 44 [4,] 36 64 64 22 [5,] 47 72 67 34 stu<-t.test(genes[,1:2],genes[,3:4]) > stu$p.value [1] 0.4198002 i get 1 pvalue for the entire col1:col2 Vs col3:col4. I am trying to get 5 p values for the 5 rows i have. I am trying to avoid a for loop coz my

Hi, I am newbie of R. I a currently using multdrc object to generate fitting curve and IC50. My 384 well format raw data contains multi dose response curves. My script goes through set of data then produce curve and ic50. Here is my sudo code: For (plateid in platelist) { Input data (plateid) as matrix Curve fitting model4logistic <- multdrc(rdata ~ ld, logDose=10) }

Hello everybody, I'm a newbie in R and just went through an introduction class recently. Here's my problem. I have 2 text files (.txt) with plain numbers ('doubles' for those who know c++) ordered into 2 columns as below: coordinate1 value1 coordinate2 value2 coordinate3 value3 ... ... coordinateN valueN I would like to write a small programme in which i would: 1. take

Hi all,   I have 5 series  (5 ts objects: rp, igpm, ereal, jurosreal, crescpib), and want to create a vector with the means of the last values of each variable. What I did was this:   mrp1<-mean(tail(rp,9)) migpm1<-mean(tail(igpm,9)) mereal1<-mean(tail(ereal,9)) mjr1<-mean(tail(jurosreal,9)) mcp1<-mean(tail(crescpib,9)) means=rbind(mrp1,migpm1,mereal1,mjr1,mcp1)   They are monthly

Hello List, I have a longitudinal samples on multiple individuals, for initial analysis, i am doing some plots to see how the variable changes with the age. In some of the individuals one or two data points are missing, IL1Ra Age.at.Sample.Collection Subject.ID 6.575466 2.004106 00709-0 NA 2.162902

I am new to R and have two scripts written slightly different but should to relatively the same thing but my lack of experience with the program I can not figure out the what I need to do to correct it. The first script gives me a consistent mean fold change values with every run but can generate negative p values for some. For the second version of the script, the fold changes seem to be very

Hi, I am trying to plot the following data so that it can be visually represented well. I tried the dotchart but I felt it was too spread out. Then I tried the barplot which is good enough for me. Is there a way to give the labels for the y-axis as in the dot chart? Also, I feel the grey level is confusing, so is there options for designs within the bars? I cannot use color as the journal wants