similar to: log2(quote(1:10)) evaluates the quoted 1:10, log() does not

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

x <- rnorm(1e6); y <- log(x); # or logb(x) or log1p(x) w <- warnings(); print(object.size(w)); ## [1] 480 str(w); $ NaNs produced: language log(x) - attr(*, "dots")= list() - attr(*, "class")= chr "warnings" y <- log2(x); # or log10(x) w <- warnings(); print(object.size(w)); ## [1] 8000536 str(w); ## List of 1 ## $ NaNs produced: language

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) # #

The derivative table resides in the function D. In S+ that table is extensible because it is written in the S language. R is faster but less flexible, since that table is programmed in C. It would be useful if R provided a mechanism for extending the derivative table, or barring that, provided a broader table. Currently unsupported mathematical functions of one argument include expm1, log1p,

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

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))) >

The issue is that without an extensible derivative table or the proposed extensions, it is not possible to automatically produce (without manual modification of the deriv3 output) a function that avoids catastrophic cancellation regardless of the working range. Manual modification is not onerous as a one-time exercise, but can be time consuming when it must be done numerous times, for example

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

Hi I am using the ggplot2 package for the volcano plot and I am using the following code for the same: g = ggplot(data=data, aes(x=data[11], y=-log10(data[12]), colour=threshold)) + + geom_point(alpha=0.4, size=1.75) + + opts(legend.position = "none") + + xlim(c(-10, 10)) + ylim(c(0, 15)) + + xlab("log2 fold change") + ylab("-log10 p-value") data[11] is a

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

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:

Hi, I'm currently in the process of writing an R-installation SOP for my company. As part of that process I'm using the recommendations from the 'R Installation and Administration' document, section 3.2, "Testing an installation". This is done on an XP machine, using the latest binary of 2.11.0. The binary is downloaded and then installed from the installer. I then

Hi, I came across an issue where some optimizations that would normally be applied to standard math function calls are not getting applied when the –ffast-math option is enabled on the Clang command line on a Linux x86_64 target. I tracked down the issue to occurring because the –ffast-math option is triggering Clang to preprocess the math.h header file with the __FINITE_MATH_ONLY__ macro set

How can I get a single backslash in a character string? My goal is to escape dots in a string that will be used as a regular expression. I thought I could do it this way: gsub(".", "\\.", x) Unfortunately, "\\" does not represent a literal backslash as I expected, but rather a pair of backslashes: > "\\." [1] "\\." > "\\" [1]

I'm having a problem when generating the following LLVM intrinsics: @llvm.exp2.f32 @llvm.log2.f32 On linux, these are available on as part of standard math libraries, the code geenrator expands them into library calls, and the linker happily finds them. However, on Windows and OSX, where no implementation exists, instead of throwing a runtime error, we get a call to a function with a null

Hi all, I was hoping to get some advice about a problem that I realize will be difficult to reproduce for some people. I'm running R 1.7.1 on an openMosix (Linux) cluster and have been experiencing some odd slow-downs. If anyone has experience with such a setup (or a similar one) I'd appreciate any help. Here's a simplified version of the problem. I'm trying to run the

Hi there, sorry for troubling everybody once again, I've got a problem rewriting Sarkar's function for rewriting the tick locations in a logaritmic way (s. http://lmdvr.r-forge.r-project.org/code/Chapter08.R): His example works for log 2 but I need log e (natural logarithm). My problem is that if I replace 2 with "e" (using paste()), I get the error message that the location

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]]