search for: log2

...guage R In the shortcut for invoking R I have set --max-mem-size=1024M, so that I get > memory.limit() [1] 1073741824 Below is an example of what keeps happening as I am working. Any suggestions as to how I can stop running out of mermory? > memory.size() [1] 502904736 > log2.harvAD <- log2.harvAD[log2.harvAD$Probesets %in% harvard.genes$probeset,] Error: cannot allocate vector of size 49 Kb > log2.harvAD <- log2.harvAD[,c(1,1+order(names(log2.harvAD)[-1]))] Error: cannot allocate vector of size 49 Kb > log2.harvAD.annot <- unlist(lapply(strsplit(names(lo...

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 know ho to grab the $log2 values with 7+ numbers. Log2HigherSeven = DataFile$l...

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 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 conc...

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 2: In ifelse(x > 0, log2(x), -log2(-x)) : NaNs produced

...low is the coding for volcano plot, i hope anybody can help me to solve the problem. #    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) # #    Notes:    Group value for control must be alphanumerically first #              Script will return an error if there are more than 2 groups # #    Load the data matrix # # Read in the .csv file data<-read.csv("file:///Users/nadya/Desktop/praktik...

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]...

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 1.5849...

...e 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) # # Notes: Group value for control must be alphanumerically first # Script will return an error if there are more than 2 groups # # Load the data matrix # # Read in the .csv file data<-read.csv("input5.csv", sep=","...

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 i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 1 minor 9.1 year...

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 the output. I assume log2() takes the log base 2 of the values? I'm not clear what -min(rel.abundance) is doing either...my hunch would be...

....nfree2fis = FALSE, randomize = TRUE, seed = NULL, ...){...} and the simplest call to this function fails: FrF2(8,4) gives the custom error message "nruns must be a power of 2.", which is generated in the first check within function FrF2: if (!is.null(nruns)){ k <- floor(log2(nruns)) if (!2^k==nruns) stop("nruns must be a power of 2.")} Would the Mac (different from all other systems) require FrF2(nruns=8, nfactors=4) ? Or what else could be the issue here ? Thanks for any pointers! Regards, Ulrike -- View this message in context: http://www.nabble....

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, &quo...

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 fa...

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? -------------- next part -------------- An HTML attach...

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 alway...

...ows 2000 system. > # Someone noticed a similar problem and reported it under ID 4459. > > # Data to reproduce... > R <- c(3.0, 3.5, 4.5, 5.0, 10.0) > T <- R > T <- 1.5*T + 0.1*(T^2) > > # Bug in lowess (third y value is wrong in lowess output)... > xin <- log2(R) > yin <- log2(T) > minVal <- min (xin, yin) > maxVal <- max (xin, yin) > plot (xin, yin, xlim=c(minVal, maxVal), ylim=c(minVal, maxVal)) > lines (lowess(xin, yin, f = 2/3, iter = 3)) > text(3.5, 2, "3rd lowess point is wrong.", col="red") > text(...

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...

...ath 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 second no . I try with different programs , but always only the first line it's going. I've tried to do this thing: In the icecast xml insert the call to the script /etc/icecast/bin/script.sh In this script I insert only 1 instruction #!/bin/bas...

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 log(c(2.12082478659910, 1.40263187453398, 1.574125429 ## 83486, -0.816399069824751, 0.215940065840533, 1.20975177084379, -0.340287874362 ## 813, 0.117151537611550, ... #...