similar to: R-beta: Re: Post-hoc tests

Hi- Is anyone working on multiple comparisons of means or post-hoc tests (ie: Tukey, Bonferroni) for R? I saw in the winter 98' archives of the R mailing lists that these tests had not been implemented yet, I was just wondering if I could look foward to having them. ;-) I also looked through the contributed packages and didn't see anything that offered such tests. I guess I could check

The Partek package (www.partek.com) allows only two selections for Multiple Test Correction: Bonferroni and Dunn-Sidak. Can anyone suggest why Partek implemented Dunn-Sidak and not the other methods that R has? Is there any particular advantage to the Dunn-Sidak method? R knows about these methods (in R 2.1.1): > p.adjust.methods [1] "holm" "hochberg" "hommel"

Hi, I have two questions want to ask. 1. If I have a matrix like this, and I want to figure out the rows whose value in the 3rd column are less than 0.05. How can I do it with R. hsa-let-7a--MBTD1 0.528239197 2.41E-05 hsa-let-7a--APOBEC1 0.507869409 5.51E-05 hsa-let-7a--PAPOLA 0.470451884 0.000221774 hsa-let-7a--NF2 0.469280186 0.000231065 hsa-let-7a--SLC17A5

Dear R community I sent a message out a while ago asking for help with multiple comparison tests for ANOVA's, but haven't had any response yet. I'm sending a final desperate plea. If I can't get this done in R I'm going to have to redo a whole lot of stuff in a commercial package, which I'm REALLY not keen to do! My problem is how to implement these tests in R. Below

Full_Name: Ludo Pagie Version: 2.8.1 OS: linux Submission from: (NULL) (194.171.7.39) p.adjust in stats seems to have a bug in handling n>length(p) for (at least) the methods 'holm' and 'hochberg'. For method 'holm' the relevant code: i <- 1:n o <- order(p) ro <- order(o) pmin(1, cummax((n - i + 1) * p[o]))[ro] where p is the

> dim(data.sub) [1] 10000 140 #####extracting all differentially express genes########## library(multtest) two_side<- (1-pt(abs(data.sub),50))*2 diff<- mt.rawp2adjp(two_side) all_differ<-diff[[1]][37211:10000,] all_differ #####list of differentially expressed genes########## > probe.names<- + all_differ[[2]][all_differ[[1]][,"BY"]<=0.01] Error in

hi list, i have to ask you again, having tried and searched for several days... i want to do a TukeyHSD after an Anova, and want to get the adjusted p-values after the Tukey Correction. i found the p.adjust function, but it can only correct for "holm", "hochberg", bonferroni", but not "Tukey". Is it not possbile to get adjusted p-values after

Hello, I've fitted a parametric survival model by > survreg(Surv(Week, Cens) ~ C(Treatment, srmod.contr), > data = poll.surv.wo3) where srmod.contr is the following matrix of contrasts: prep auto poll self home [1,] 1 1 1.0000000 0.0 0 [2,] -1 0 0.0000000 0.0 0 [3,] 0 -1 0.0000000 0.0 0 [4,] 0 0 -0.3333333 1.0 0 [5,] 0 0

I append below a suggested update for p.adjust(). 1. A new method "yh" for control of FDR is included which is valid for any dependency structure. Reference is Benjamini, Y., and Yekutieli, D. (2001). The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 29, 1165-1188. 2. I've re-named the "fdr" method to "bh" but

Estimados herreros, Sabéis si hay algún sitio donde pueda hacer una pregunta sobre estadística, en concreto un diseño experimental. Alguna lista, foros, etc. Ya se que este no es el sitio adecuado para preguntas de estadística, pero por si alguien se pica os la pongo a continuación. Dos tratamientos C y H. Se aplican a una serie de especies (p.e. 10) Se observa la respuesta de las especies a

Hi, I was trying to figure out how to do post-hoc tests for Two Way ANOVAs and found the following 2 approaches: a. Do pairwise t-tests (bonferroni corrected) if one finds significance with the ANOVA. Link- http://rtutorialseries.blogspot.com/2011/01/r-tutorial-series-two-way-anova-with.html b. Do TukeyHSD on an aov model Link-

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I have been using SAS for some time, and now I have discovered R. I am very happy with it, but I have not found out how to perform some of the multiple comparisons I was used to do in SAS. With the SAS/STAT, I generally used the MEANS (for comparison of arithmetic means) and the LSMEANS (for adjusted means) statements of the GLM procedure (I

Dear R people, I have a couple of questions about post-doc analyses for 2 by 2 within subjects ANOVA. I conducted a psycholinguistic study that combined a 2 by 2 design and a latin square design. Specifically, I had 32 items each of which generated 4 conditions. Participants saw each of the 32 items only once: 8 in Condition A, 8 in B, 8 in C, and 8 in D. The table below serves as an example.

Hi- Is anyone working on multiple comparisons of means or post-hoc tests (ie: Tukey, Bonferroni) for R? I saw in the winter 98' archives of this mailing list that these tests had not been implemented yet, I was just wondering if I could look foward to having them. ;-) I also looked through the contributed packages and didn't see anything that offered such tests. I guess I could check for

Hi all. New to this list so ... sorry if this is old, but I have searched honest. I have been asked to install samba on some (60) macintoshes. The macs run OSX10.2. I have the developer tools and samba 3.0.0. Configure works but make crashes out with libsmb/clikrb5.c139: #error UNKNOWN_GET_ENCTYPES_FUNCTIONS followed by 4 more errors ((caused by the first?). I cant see any ref to this or options

Hello, we've been more than happy with Samba 3.0.22 on our Solaris 9 machines, but when we upgraded to Solaris 10 users are experiencing a multitude of XP desktop problems: icons disappear, start menu will hang because a few items link back to a samba share, many XP windows write delay problems, the whole desktop will hang. It seems the samba server will stop responding. Is there anybody out

Hello, I have a dataset with 4 variables, each consisting of a vector, all with the same length. I start by interpolating the first three variables using the function "interp", and plot the interpolation successfully using "filled.contour". I then interpolate the first two variables and a fourth using "interp" again, but when I try to overlay the contour lines

Hello, We use LDAP to store our Maildir++ quota information for our Maildir mailboxes. I notice in the documentation that only SQL and flat files are supported by the dictionary quota if I want to use quota with mdbox? Are there any plans to allow LDAP to be used as the store? Regards, Matthew. -- Dr Matthew Williams MEng PhD MBCS Systems Administrator - IT Services - Bangor

Dear all, I run a kruskal wallis test and found significant results. Then, I conducted all pairwise comparisons and found no significant results. Could anyone please give me a hint as to why this happens or redirect me towards a specific web page where I can find more info? (I used alpha=5% and made no bonferroni or other correction for the pairwise comparisons) Thank you   Dr. Iasonas

I'm in the process of trying to track down the cause of frequent Delayed Write Failures on our network. Most seem to be from database-like files (e.g. firefox/thunderbird sqlite files) that are stored in the users Application Data directory. The AppData directory in our case is on a mapped network drive and excluded from the set of files copied back and forth as part of the roaming