search for: dye

I am a novice R user, and have been in trouble to get the right mixed model syntax in microarray analyses. There are three factors: Dye(2 levels), Temperature(3 levels) and Array(3 for each Temperature with a total of 9 arrays). I want to treat array as random, and to regard array variation different between Temperatures. So the model I want to seek is: Y = Dye + Temp + Dye + Temp*Dye + Array(Temp) + Dye*Array(Temp). For F tests...

Hello R-users, I am currently trying to learn how to use the function gls of the nlme library. I fitted the following model: Generalized least squares fit by REML Model: response ~ array + dye + genes + variety + variety * genes + array * genes + dye * genes Data: data I have 11 arrays, 2 dyes, 2 varieties, 3200 genes, and 2 replications for each. Therefore I should have the corresponding degrees of freedom and number of coefficients, but instead I have the following: Coefficients: (I...

Hi all, when i run this script: >read.table("Angelika.txt",header=T,sep="\t") >mytable=read.table("Angelika.txt",header=T,sep="\t") >for ( dye in c("A","B","C","F","G","K","L","M")) + { + for (cond in 1:8) + { + measurement = table[mytable[,"bed"]==cond & mytable[,"dye"]==dye,"differenz"] +...

...unequal length, I'd like to pair each element of the shorter vector with an element of the longer vector such that the sum of squared differences between the pairs is minimized. Can someone point me to an R function or an algorithm for accomplishing this? All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com [[alternative HTML version deleted]]

...:session library(ggplot2) wind.data <- read.csv("pmrf_windrose_info_new.csv") wind <- ggplot(wind.data, aes(x = degree, y = time, fill = wind)) wind.bar <- wind + geom_bar(stat = "identity") wind.bar + coord_polar() #+end_src All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com [[alternative HTML version deleted]]

hi all got a windows 2008 server using samba as a primary domain controller. also got terminal services on the windows box for remote desktops, got some clients set up with thinstation to automatically connect to the terminal server with rdesktop. got a problem with logging on and off, its taking about 2 minutes to log in, "please wait for the user profile service", time increases if

...rix. How do I construct the matrix[f1,f2xf3] from my data frame? Also, any pointers to existing code that performs multi-way median polish will be appreciated. Sorry for the newbie-type query, but manipulating data prior to analysis is really hard for me in R. All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com [[alternative HTML version deleted]]

...(v,w), (u,w). I want a DAG with only intransitive relations. Can someone point me to an R function that will take my adjacency matrix and give me back one with only intransitive relations? In the example, I'd like to get rid of (u,w) and keep (u,v) and (v,w). All the best, Tom -- Thomas S. Dye http://www.tsdye.com

...(TS)(i,k) are random effects whereas the rest are fixed effects. How do I specifiy the random part of the model formula in lme(), especially concerning the combined effect (TS)? Moreover, when I run the model as a fixed effect model I get the following error: > lm(logMed ~ lenAA + TREAT + DYE + SLIDE + SLIDE:DYE,data=MA) Error in lm.fit(x, y, offset = offset, ...) : NA/NaN/Inf in foreign function call (arg 4) However, when I run the model with a reduced data set it works. In the first case I have 16512 data points whereas in the reduced case I use only have of it. Do I reach...

Greetings, I have a service running on a Windows Server 2003 box that I want to write to a Samba share running on Solaris 10. The Samba is not a DC. How can I give access to the Local System user on the Windows box without making the share writeable to any other user or system? Regards, KB ________________________________ Notice of Confidentiality: The information contained in this

I''m having issues with HVM live migration and every xen version I''ve tried - 3.0.1, 3.1.x, 3.3.0 and 3.3.1. Migrations will fail intermittently with messages like this on the receiving hypervisor: [2009-02-02 11:35:19 12629] DEBUG (XendCheckpoint:264) [xc_restore]: /usr/lib64/xen/bin/xc_restore 4 4 2 3 1 1 1 [2009-02-02 11:35:19 12629] INFO (XendCheckpoint:403)

...unif(0,100) + sigma2.btw<-sigma.btw*sigma.btw + tau.btw<-1/sigma2.btw + } > ########################################## > inits = function() + list(theta=1500, tau.with=1, sigma.btw=1) > ########################################## > setwd('C:/Users/ethan/Desktop/Dissertation/R/Dyes') > > print(dats) $batches [1] 6 $samples [1] 5 $y [,1] [,2] [,3] [,4] [,5] [1,] 1545 1555 1605 1465 1625 [2,] 1440 1490 1510 1545 1520 [3,] 1440 1560 1560 1595 1455 [4,] 1520 1495 1445 1630 1450 [5,] 1580 1595 1440 1515 1480 [6,] 1540 1550 1595 1635 1445 > bugs.data(dats) [1...

I have a customer that is using 250 gig drives for his business data. I have been using rsync to keep mirror copies of his data on a second machine. In the last 3 months I have lost 2 of four drives, the last one being the system drive. I have been doing a manual switchover. Each time rsync runs, I copy my samba conf files, passwd, shadow and group files from etc. Has anyone setup a HA

I have been setting up my domain server using FC2 and samba 3.0.9. First thing, for your information: In the notations in several sources, it tells you to user "logon path = \\%L\profiles\%u" this is wrong. It should be, "logon path = \\%L\profiles\%U". Now that I spent 5 million hours banging my head on a wall with that, how do I get he exist desktops on my 2000/XP

Hello all, I have data: Genes time rep vart dye y trt 130911 sa1-d07 030min 1 col g 9.636244 o 145771 sa1-d07 030min 1 col r 8.107577 c 93335 sa1-d07 030min 1 ler g 7.409566 o 94821 sa1-d07 030min 1 ler r 5.107160 c 10119101 sa1-d07 030min 2 col g 8.336862 o 11605101 sa1-d07 030min 2 c...

Recently I started noticing that after running for a while puppetmaster would freeze after a client called `freshness` which would eventually result in the client getting a timeout and the client dyeing. I tracked the freeze down to the call to ActiveRecord::Base.verify_active_connections! in rails.rb on line 26. After scouring the nets I finally found: http://groups.google.com/group/activemessaging-discuss/browse_thread/thread/7cbbcd761fcb0fd8 which led me to the mongrel faq: http://mongre...

...book under Windows. I suspect by(.) to be a poor implementation for doing individual analysis on subgroups. Is there an alternative and more efficient way for doing by-group processing within lme(.). Here some code to give you a glimpse gfit <- by(longdata, gen, function(x) lme(fixed=response ~ dye + C(treat, base = 4 ), data=x,random =~ 1 | slide) ) Thanks in advance & regards Gerhard Krennrich ------------------------------------------------------------------------ BASF Aktiengesellschaft GVC/S - B009 Gerhard Krennrich Tel.: +49 621 60-78299

Hello, I use lme4 package. library(lme4) fit=lmer(y ~ time+dye+trt+trt:time + (1|rep), data=dataset, na.action='na.omit') anova(fit) The anova gives sequential F-tests and sequential SS. My question is: how I can get partial F-tests and partial SS? For lm (not lmer) anova(lm(y~x+z)) we can use anova(fit, ssType=3) but it is not work for lmer. Na...

Dear R helpers, I am working with R 2.4.1 GUI 1.18 (4038) for MacOSX. I have a matrix of 10 000 genes and try to run the following commands: > model.mix<-makeModel (data=data, formula=~Dye+Array+Sample+Time, random=~Array+Sample) > anova.mix<-fitmaanova (data, model.mix) > test.mix<-matest (data, model=model.mix, term="Time", n.perm=100, test.method=c(1,0,1,1)) I get the following error message: Doing F-test on observed data ... Doing permutation. This may...

Does anyone have nice quality controlls for affy arrays,.... Can't find any tools as are being used for 2 dye arrays..... cheers, marinus This e-mail and its contents are subject to the DISCLAIMER at http://www.tno.nl/disclaimer/email.html [[alternative HTML version deleted]]