similar to: use one way ANOVA to select genes

Hi Others can have better insight in your question so i tis preferable to post your mails to the Rhelp list too. I hope your datafile is all numeric. If not after t(datafile) can be character. AFAIK your pvalue is not propagated to aov function. Based on artificial data your construction arrives to result, which in this case tells you that there is almost no difference in those 5 groups.. m

Hi Duncan The simples spreadsheet is: Put a name in the cell, let say "a1" Put number e.g. 1 below "a1" Copy the number to enough rows Select this column and press ctrl-c result is > temp<- read.delim("clipboard") > str(temp) 'data.frame': 1513 obs. of 1 variable: $ a1: Factor w/ 2 levels "1","a1": 1 1 1 1 1 1 1 1 1 1 ...

Dear all I have 3 questions. Due to some reason I switched from Vista to Ubuntu on home PC. I was used to start with Rgui.exe. However I am not able to find it under Ubuntu and R starts as terminal (probably Rterm). Question 1. Is Rgui.exe available on linux? In Windows doc folder I can find manuals, however I did not find doc folder in Ubuntu. I found somewhere that manuals need to be

Dear all I am struggling to fit data which form something like CDF by lognorm. Here are my data: proc <- c(0.9, 0.84, 0.5, 0.16, 0.1) size <- c(0.144, 0.172, 0.272, 0.481, 0.583) plot(size, proc, xlim=c(0,1), ylim=c(0,1)) fit<-nls(proc~SSfpl(size, 1, 0, xmid, scal), start=list(xmid=0.2, scal=.1)) lines(seq(0,1,.01), predict(fit, newdata=data.frame(sito=seq(0,1,.01))), col=2) I tried

Hi Petr; Thanks for your reply. It is much appreciated. A small example is given below for 4 independent and 4 dependent variables only. The values given are regression coefficients.I have looked ggplot documents before writing to you. Unfortunately, I could not figure out as my experience in ggplot is ignorable Regards. Greg y1 y2 y3 y4 x1 -0.19 0.40 -0.06 0.13 x2 0.45 -0.75 -8.67 -0.46 x3

Hello, I am trying to use varcomp to decompose the variance across multiple nested levels on a lme object. I am able to successfully do this and when I view the varcomp object I can see the individual values / estimates for the variance at different levels. However, I want to be able to extract each of them separately, as I need to build a confidence interval using bootstrapping on the sample

Hi Petr; Thanks so much. Exactly this is what I need. I will play to change color and so on but this backbound is perfect to me. I do appreciate your help and support. Regards, Greg On Thu, Feb 8, 2018 at 1:29 PM, PIKAL Petr <petr.pikal at precheza.cz> wrote: > Hi > > I copied your values to R, here it is > > > > > dput(temp) > > > > temp <-

Hi > -----Original Message----- > From: Robert Baer [mailto:rbaer at atsu.edu] > Sent: Wednesday, August 16, 2017 3:04 PM > To: PIKAL Petr <petr.pikal at precheza.cz>; Duncan Murdoch > <murdoch.duncan at gmail.com> > Cc: r-devel at r-project.org > Subject: Re: [Rd] strange behaviour read.table and clipboard > > You said, "put a name in the cell".

Hi Petr; I would like to get a plot with names as they are in the original file. They are chemical names and I have 733 in the my file. For example, let me give to chemical names "*2-hydroxybutyrate/2-hydroxyisobutyrate*" and "*palmitoyl-arachidonoyl-glycerol (16:0/20:4) [1]**" .So, what should I put [c(2,3,1)] part in the command: iris$MySpecies<-factor(iris$Species,

Hi all; I have 733 discrete categories that will go on y-axis in ggplot2. I used the following command to put the name of x-axis. scale_x_discrete (limits = c("SI", "HOMAIR", "AIR","HOMAB","SG","DI","FI","FG")) Since there are only 8 categories on x it was easy to do. Is there any way to do the same for 733 discrete

Dear friends - I have a data.frame with "," instead of "." and found the discussion http://r.789695.n4.nabble.com/How-to-replace-all-commas-with-semicolon-in-a-string-tt4721187.html#a4721192 so copying the code of Ulrik(I hope:-)) I tried (making some data) AX <-

Dear all I used to transfer data from excel to R by simple ctrl-c and read.delim("clipboard") construction. I know it is a bad practice but it is easy and for quick exploratory work it is OK. However after changing to new R devel few days ago I encountered weird behaviour. I tried one or two columns. In case of 2 columns, header is repeated after 526 items >

Hi all, ok I have this issue: I want to change my graphs legends to custom text, often requiring the use of superscripts/subscripts I tried to use this instruction I found on stack overflow: labs(x = "R(Ohm)", y= "CDF", aesthetic= " Content (%)" ) but it wont' seem to work. Also tried bquote for super/ subscripts xlab(bquote(~x~/(~x~ + ~MO[2]~)*

Generate a clustered pattern in [0; 1]2 as follows: (a) Generate nc, say 20, independent cluster centres (which can be called parents) that are distributed i.i.d. uniformly in the unit square; (b) then n daughters are assigned i.i.d. uniformly to these parents and such that each daughter is located i.i.d. uniformly in a disk of radius r = 0:1 centred at her parent, under the periodic boundary

Dear all, I would appreciate please a piece of help regarding the use of acast/dcast functions in reshape2 package. Specifically, I'm working with a data frame, that has information about SAMPLE, GENE, and TYPE of MUTATION (as shown below): Sample Gene Type 22M AEBP1 SNV 17M AEBP1 SNV 22M ATR INDEL 22M ATR SNV 11M BTK SNV 11M BTK

> x [1] 8.0 7.9 7.5 7.0 8.0 7.3 8.0 7.2 7.4 7.3 7.8 8.0 7.7 8.3 7.8 7.8 7.1 7.7 6.9 7.5 7.5 7.3 7.2 7.5 7.2 > stem(x) The decimal point is at the | 6 | 9 7 | 012223334 7 | 5555778889 8 | 00003 > y <- c(x, 8) > stem(y) The decimal point is 1 digit(s) to the left of the | 68 | 0 70 | 00 72 | 000000 74 | 00000 76 | 00 78 | 0000 80 | 00000 82 | 0 The

Thanks. I thought lm() function is for linear model, such as the correlation below: Y= aX + b On Wed, Jun 14, 2017 at 5:25 PM, MacQueen, Don <macqueen1 at llnl.gov> wrote: > Start with the lm() function; i.e., see > > ?lm > > -Don > > -- > Don MacQueen > > Lawrence Livermore National Laboratory > 7000 East Ave., L-627 > Livermore, CA 94550 >

I did the same transition, facing the same issues, so I settled for installation of RKWard. This pretty much reproduces my previous experience with Tinn-R and the Rgui. HTH Ruben ________________________________ Ruben H. Roa-Ureta, Ph. D. Senior Scientist, Center for Environment and Water, Marine Studies Section, King Fahd University of Petroleum and Minerals, KFUPM Box 1927, Dhahran 31261,

Hi all, I would like to have help in getting annotation ticks (corresponding to the minor grid) on my plot. Here is my toy example : par(mar=c(5, 6, 5, 5) + 0.1) x<-1:10 y<-x^2 plot(x,y,log="xy",xlab="log(x)",ylab="log(y)") par(new=T)

Hi Dear all; I would like to create a plot for regression coefficients with each independent variable (x) along the side and the phenotypes (y) across the top (as given below). For each data point, direction and magnitude of effect could be color and significance could be the size of the circle? Is this possible? I would greatly be appreciated your help. Thanks, Greg y1 y2 y3 y4 y5 y6 x1