[R] qvalue package: checking I'm using the right output values.

Can I ask, when I run the below code: library(qvalue) pvals <-c(0.01,0.02,0.03,0.10,0.67,0.08,0.55,0.10,0.81,0.08,0.94,0.10,0.81,0.08,0.72,0.10,0.22,0.08,0.72,0.01,0.02,0.03,0.04,0.05,0.06,0.07,0.01,0.02,0.03,0.10,0.67,0.08,0.55,0.10,0.81,0.08,0.94,0.10,0.81,0.089,0.72,0.10,0.22,0.08,0.72,0.01,0

[R] Fwd:

Dear all, I am hoping to use the mt.maxT package, so I'm trying to understand how the maxT algorithm works in the multtest package. I have an example of data: SNP1 p value= 0.02 SNP1 permutation p values = 0.03, 0.03, 0.03, 0.04, 0.04. SNP2 p value =0.03 SNP2 permutation p values = 0.4,0.5,0

[R] egscore - lambda will not go below 1.1

Hi all, I want to associate mortality with ~100K SNPs, in 6,500 samples that are divided up into 60 breeds. So it's important to account for population stratification in my analysis. I'm using egscore (the eigenstrat method) for the association (and I've tried using the polygen and grammar packa

[R] convert.snp.ped in GenAbel

Having a problem with convert.snp.ped in GenABEL (on linux). My map file looks like this (tab-separated) (called Genotype.map) chrom name position 13 SNP1 39703523 My ped file looks like this (Called Genotype.ped) PF1 PF1 0 0 2 -9 C C PF2 PF2 0 0 2 -9 C A PF3 PF3 0 0 1 -9 C C PF4 PF4

Re: [R] Cox model -missing data.

model but not completely remove the row? This is more what I was hoping someone would know if it's possible to incorporate into the model I described above? Thanks On Fri, Dec 19, 2014 at 10:21 AM, Ted Harding wrote: > > Hi Aoife, > I think that if you simply replace each "*&q

[R] Cox model -missing data.

Hi all, I have a data set like this: Test.cox file: V1V2 V3 Survival Event ann 13 WTHomo 41 ben 20 *51 tom 40 Variant 61 where "*" in

Re: [R] exclude missing co-variable data in cox model

Hi all, I have a data set like this: Test.cox file: V1V2 V3Survival Event ann 13 WTHomo 41 ben 20 *51 tom 40 Variant 61 w

Re: [R] R shell script

ctly? You probably > need > > list.files(pattern = ".out") > > to get started. Then just wrap your script in a function and pass it > to (s|l)apply something like: > > sapply(list.files(pattern = *.out"), function(x) wilcox.test ( ... ) ) > > Michael >

[R] R shell script

ke this shell script. Any help appreciated :) Aoife [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-g

[R] check for difference.

Hello I have two lists of numbers, each list is ~800 numbers long. I want to know if the two lists are significantly different from each other. Could anyone suggest what library in R to use? I think maybe the mann-whitney test, as it is not parametric, but i am unsure if it is suitable as my list

[R] plot columns

lar columns and plot? i was looking at this: https://stat.ethz.ch/pipermail/r-help/2007-July/137638.html but i can't seem to alter it to my needs Thank you Aoife [[alternative HTML version deleted]] __ R-help@r-project.org mailing l

[R] (no subject)

ot;codon2", "codon3"))) Library(ca) plot(ca(table)) is there a way that i can see the "second principal axis" of this analysis? Aoife [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://s

Re: [R] max.print

Hey i have a similar size dataset and ran into the same problem, but i found this command works fine: options(max.print=100) to fix it? On Sat, Mar 10, 2012 at 4:35 PM, sybil kennelly wrote: > Dear all. > > I wanted to read in a 20,000 row X 60 column matrix (called "table") into > R. > >

Re: [R] help please. 2 tables, which test?

ure to answer your question is like > buying a new suit then having plastic surgery to make you fit the suit > rather than having the tailor modify the suit to fit you. > > If you can give us more information about what your question is we > have a better chance of actually helping y

Re: [R] help please. 2 tables, which test?

Thank you. Can the chi-squared test compare two matrices that are not the same size, eg if matrix 1 is a 2 X 4 table, and matrix 2 is a 3 X 5 matrix? On Fri, Mar 9, 2012 at 4:37 PM, Greg Snow <538...@gmail.com> wrote: > The chi-squared test is one option (and seems reasonable to me if it > the t

Re: [R] layer plots.

Many thanks for reply. I have trouble understanding how to use response, i am sorry. My question is i have two matrices. I then plot two matrices. Then I have 2 seperate plots. I can color the nodes in the plots in two different colors. Then, how do i merge the two plots to view one overlapping the

Re: [R] Plotting shaded areas

May I ask, is it possible using plotrix to shade a group of variables differentially from the rest of a graph, eg so the output looks similar to this, where the nodes of open circles are my nodes of interest: http://r.789695.n4.nabble.com/file/n4459137/Screen_shot_2012-03-08_at_12.18.34.png Man

Re: [R] find points on a graph

May i please update my question, and I understand now something that i did not yesterday. In this example: table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1", "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2",

Re: [R] find points on a graph

Thank you. I really appreciate the help. May i ask two questions. In the example below: table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1", "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2", "codon3"))) Libr

Re: [R] find points on a graph

e graph, and either highlight them a different color, or draw a border/shade them in some way. basically highlight them in any way? is this any more helpful to explain what i mean? Aoife -- View this message in context: http://r.789695.n4.nabble.com/find-points-on-a-graph-tp4452746p4453046.html

[R] find points on a graph

Hey guys, Can anyone help? I did a correspondance analysis and made a plot. I also have a specific list of nodes that i want to find in my plot and want to either color the nodes that appear in my list differently, or put some kind of border around that group of nodes... Would anyone know how t

[R] codon usage bias

ta ttc ttg ttt NA NA NA NA it's telling me that there are no codons. I'm not sure how to split up the data or make this work at all. Any help appreciated. Aoife -- View this message in context: http://r.789695.n4.nabble.com/codon-usage-bias-tp4431740p4431740.html Sent from the

Re: [R] Installing rgl

Thank you for the reply, my problem is that i don't understand the error that plot(ca) is giving me: > plot(ca) Error in matrix(as.matrix(obj), nrow = I, ncol = J) : non-numeric matrix extent so just to put this in context: my workscreen looks like this: > table A B C G1 1 34.0

Re: [R] Installing rgl

analysis results into a graph? Basically i just want to picture this correspondance analysis results graphically, using any method :( Aoife -- View this message in context: http://r.789695.n4.nabble.com/Installing-rgl-tp865867p4410184.html Sent from the R help mailing list archi

Re: [R] Installing rgl

libname, pkgname) : error in rgl_init and when you look in the library for rgl you get: > library(rgl) > Would anyone know (in simple language, i'm a biologist, not a statistician :( ) either how to fix this, or an alternative package that will do a simple correpondance analysis on a

[R] basic help: graph multivariate analysis.

know if its not) I want to plot these multivariate results on a graph. i have read through various pdf's (e.g. using r for data analysis and graphics and simple R) but i'm still stuck. Could anyone help explain the commands needed to turn the above data into any sort of graphical form?