Displaying 20 results from an estimated 1000 matches similar to: "Are post-hoc tests being developed for R?"
1998 Jul 16
1
R-beta: Re: Post-hoc tests
Matt,
Here's a Bonferroni-corrected multiple one-sample t-test that I wrote
some years ago. It took a while to get it into R, as na.omit doesn't
seem to handle vectors and I had to write a quick kludge (na.remove).
Another more general point was that I discovered that the help page for
t.test gives the name "parameters" for the degrees of freedom, as in S.
However, the name
2005 Jul 14
2
Partek has Dunn-Sidak Multiple Test Correction. Is this the same/similar to any of R's p.adjust.methods?
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"
2011 Oct 04
1
a question about sort and BH
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
2009 Feb 11
1
p.adjust; n > length(p) (PR#13519)
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
2008 Mar 01
2
Newbie: Incorrect number of dimensions
> 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
1998 Jul 13
0
R-beta: Post-hoc tests for R??
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
2005 May 15
3
adjusted p-values with TukeyHSD?
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
2001 Feb 08
2
Test for multiple contrasts?
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
1999 Nov 25
0
desperate!
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
2013 Feb 13
5
off topic ¿comparaciones múltiples?
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
2005 Jan 16
1
p.adjust(<NA>s), was "Re: [BioC] limma and p-values"
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
2012 Oct 19
2
Post Hoc tests for ANOVA
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-
2005 Sep 15
3
means comparison in R (post-hoc test)
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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
1998 Jul 08
1
R-beta: POSIX and regcomp on SGI-IRIX 5.3
Hey Guys,
I'm trying to install R on an SGI IRIX 5.3 machine. I'm having trouble
getting R to use POSIX regular expressions. Here is the error message I get
when I run help:
> help()
Error in gsub(pattern, replacement, x, ignore.case, extended) : POSIX regular
expressions not available
I looked through the R-help archives and I found a few tips concerning the
problem. I tried them
2010 Jun 06
1
Why did TukeyHSD not work when I used it for post-hoc for 2way within-subjects anova?
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.
2012 Jan 12
2
kruskal wallis post hoc?
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
2008 Dec 14
1
how to convert factors to numbers
Hello, I am relatively new to using R. I am using R version 2.8.0. I have a
program that downloads stock data from Yahoo! Finance and stores it to a
text file on my hard drive. The text file contains the date, opening price,
high price, low price, closing price, volume and adjusted price (i.e.,
adjusted for dividends and splits). I want to read and manipulate the data
in R. However, when I
2011 Jun 12
1
welch anova and post-hoc
dear r community...
it loks like i won't be able to reach homogenity of variance for my
dataset, so i end up with welch anova instead of regular anova.
documentation on this test is rather scarce, so maybe someone here can
enlighten me a bit:
- do i understand that no two-way implementation of the welch anova
has been developed yet?
- is there a post-hoc test for welch anovas implemented in
2012 Oct 24
2
Kaplan Meier Post Hoc?
This is more of a general question without data. After doing 'survdiff',
from the 'survival' package, on strata including four groups (so 4 curves
on a Kaplan Meier curve) you get a chi squared p-value whether to reject
the null hypothesis or not. Is there a method to followup with pairwise
testing on the respective groups? I have searched the library but have
come up with
2013 May 14
1
Post hoc test for GLM with poisson distribution
Hi R-people,
I performed controlled experiments to evaluated the seeds germination of
two palms under four levels of water treatments. I conducted a generalized
linear model (GLM) with a Poisson distribution to verify whether there were
significant differences in the number of seed germination (NS-count
variable) between treatments and species (explanatory variables). Thus, my
model and output