similar to: question about precision, floor, and powers of two.

Dear R users, according the help(log), the function log2(x) should give the natural logarithm of x. I expect in case of x=2 to to get 0.6931, however, R gives me 1 as a result. Similar, logb(2,2) gives 1 again. I'm wondering if I have missed something ? Yours Frank -- Frank Mattes, MD e-mail: f.mattes at ucl.ac.uk Department of Virology fax 0044(0)207 8302854 Royal Free Hospital

I'm attempting to compile and install R version 1.7.1 for my statistical geneticists. It seems to compile correctly -- that is, it compiles without errors -- but the regression test is failing in the following manner: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > ## log > stopifnot(all.equal(log(1:10), log(1:10, exp(1)))) > stopifnot(all.equal(log10(30), log(30, 10))) >

Hello, R users, I have two factors (treat, section) anova design experiment where there are 3 replicates. The objective of the experiment is to test if there is significant difference of yield between top (section 9 to 11) and bottom (section 9 to 11) of the fruit tree under treatment. I found that there are interaction between two factors. I wonder if I can contrast means from levels of

I have a function that, among other things, runs a linear model and returns r2. But, the number of predictor variables passed to the function changes from 1 to 3. How can I change the formula inside the function depending on the number of variables passed in? An example: get.model.fit <- function(response.dat, pred1.dat, pred2.dat = NULL, pred3.dat = NULL) { res <- lm(response.dat ~

Dear R-users, I have a basic question about how to determine the antilog of a variable. Say I have some number, x, which is a factor of 2 such that x = 2^y. I want to figure out what y is, i.e. I am looking for the antilog base 2 of x. I have found log2 in the Reference Manual. But I am struggling how to get the antilog of that. Any help will be appreciated! > version platform

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

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

Hi, I am using R for microarray data anlaysis. When I normalize my data, it converts all my data in to log base 2 values. how can I convert back to log base 10..is there any function in R which I can use or how can I take anti log. or is there any function in R for antilog. Please let me know,..if anyone knows.. Thank you so much, Saurin ===== Saurin's WebWorld:

I have question about log2 transformation and performing mean on log2 data. I am doing analysis for ELISA data. the OD values and the concentration values for the standards were log2 transformed before performing the lm. the OD values for samples were log2 transformed and coefficients of lm were applied to get the log2 concentration values. I then backtransformed these log2 concentrations and the

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

Dear all, I just noticed that the 0.9 update for FrF2 did not work out for Mac OS due to an error in an example that ran without error on all other platforms. I do not find any reason for this. In the past, umlauts or tab characters have sometimes been an issue, but I didn't find any of these. The function definition is FrF2(nruns = NULL, nfactors = NULL, factor.names = if

It's not a big deal, but it always annoyed me a bit when I hit it, so I'll bring it up here. LLD represents an alignment X as log2(X) in some places and just X in other places. It's a bit confusing. Because I always think alignments in my mind in terms of 1, 2, 4, 8, ..., instead of 2^1, 2^2, 2^3, ..., I'd like to propose to always use real values. Any objections? --------------

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

Dear R community, I have trouble implementing a nested variance-covariance matrix in the lme function. The model has two fixed effects called End and logpgc, the response variable is the logarithm to base 2 of Intensity ( log2(Intensity) ) and the random effects are called Probe and ProbeNo. The model has the following nesting structure: A Pixel is nested within the ProbeNo,the ProbeNo is

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