Displaying 20 results from an estimated 700 matches similar to: "how to do multiple comparison in the nonparametric statis tical analysis?"
2005 Oct 11
1
STATIS
Hi, i'm having trouble using Statis in ADE4 package.
I want to study a matrix with 18x414...could any body help me?!?!'
Urgent
Thanks
Miguel Ribeiro
Portugal
[[alternative HTML version deleted]]
2006 Jun 21
1
eliminating a do loop
Using a "by() statement, I am preparing ANOVA's for multiple experiments,
and using simint() to generate confidence intervals.
This works fine.
simint.by.fit <- by(analytes.dfr, list(Assay = analytes.dfr$analyte ),
function(data) (simint(value ~ tx, data = data,type='Tukey' ) ) )
I can separately prepare plots of the confidence intervals, and I can
prepare separate plots
2012 Dec 15
1
Statis of www.hdt-project.org/wiki/hdt-0.5.0 site?
Noticed that the sites has not been responding correctly for a few
days, and was wondering if anyone knew what was up.
traceroute and ping get to the ip, but website times out after a
very long time.
+----------------------------------------------------------+
Michael D. Setzer II - Computer Science Instructor
Guam Community College Computer Center
mailto:mikes
2003 May 13
0
Robert Gentleman's talk to the Statis. Soc. of Canada
Users of R may find the "Message from the President" in the latest issue
of Liaison, the newsletter of the Statistical Society of Canada, to be
of interest. (http://www.ssc.ca/documents/pubs/Liaison17.2.pdf). In
this message Jim Ramsey, President of the SSC, describes his purpose
in inviting Robert Gentleman to give the President's Invited Address
at their annual general meeting.
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
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
2003 Jun 16
3
Constrained optimization
Greetings, R-Wizards:
I'm trying to find an extremum subject to a nonlinear constraint. (Yes, I
have perused the archives but have found nothing positive.) The details of
the problem are these:
In a paper published some years ago in Technometrics, ("Confidence bands for
cumulative distribution functions of continuous random variables"
Technometrics, 25, 77-86. 1983), Cheng and
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
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
2004 Dec 19
1
limma, FDR, and p.adjust
I am posting this to both R and BioC communities because I believe there
is a lot of confusion on this topic in both communities (having searched
the mail archives of both) and I am hoping that someone will have
information that can be shared with both communities.
I have seen countless questions on the BioC list regarding limma
(Bioconductor) and its calculation of FDR. Some of them involved
2004 Dec 19
1
limma, FDR, and p.adjust
I am posting this to both R and BioC communities because I believe there
is a lot of confusion on this topic in both communities (having searched
the mail archives of both) and I am hoping that someone will have
information that can be shared with both communities.
I have seen countless questions on the BioC list regarding limma
(Bioconductor) and its calculation of FDR. Some of them involved
2008 Mar 09
2
p-adjust using Benjamn and Hochberg
Hello,
I am trying to use the p.adjust function for multiple testing.
here is what i have
9997 201674_s_at 0.327547396
9998 221013_s_at 0.834211067
9999 221685_s_at 0.185099475
I import them from excel have have the gene symbol as well as the pvalue
here is the issue
> pa<-p.adjust(pt,method="BH")
Error in p[nna] : object is not
2011 Sep 21
3
Quelplot
Hi all,
Does anyone have an R implementation of the queplot (K.?M. Goldberg
and B.?Iglewicz. Bivariate extensions of the boxplot. Technometrics,
34(3):pp. 307?320, 1992)? I'm struggling with the estimation of the
asymmetry parameters.
Hadley
--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/
2005 Oct 28
2
Uncensoring a dataset - resent
Does anyone know of an R package that I can use to uncensor a normal or
log-normal dataset? I'm particularly interested in the MLE method of
Cohen (1959), "Simplified estimators for the normal distribution when
samples are single censored or truncated," Technometrics, 1(3), 217-237.
Of course, if there is anything better, I'd be glad to hear about that
too.
Thanks.
Rick
2002 Oct 30
1
typo in p.adjust (PR#2231)
Full_Name: Peter Ehlers
Version: 1.6.0
OS: Windows 2000 Pro
Submission from: (NULL) (136.159.61.178)
In:
p.adjust package:base R Documentation
In the paragraph:
Hochberg's and Hommel's methods are valid when the hypothesis tests
are independent or when they are non-negatively associated (Sarkar,
1998; Sarker and Chang, 1997). Hommel's method is
2003 Apr 03
1
Tukey's one degree of freedom for nonadditivity?
Is there code available to decompose interactions involving at least
one nominal factor with more than 2 levels as described, e.g., by Tukey
or by Mandel (1971, Technometrics, 13: 1-18)?
Tukey's model:
E(y[i,j]) = mu0 + a[i] + b[j] + c*a[i]*b[j],
estimating a, b, and c so sum(a) = sum(b)= 0. Mandel essentially
describes a singular value decomposition of the interaction.
Thanks,
2003 Sep 11
1
S+DOX eqivalent in R?
Dear List,
I am looking for a function `Pseudo standard error' (PSE), which is
available in S+ DOX (design of experiemnt) module - Is there a similar
function available in R?
Reference for PSE function is in the paper:
'Quick and easy analysis of unreplicated factorials' by Russell V. Lenth,
Technometrics, 1989, 31, 4, 469-473.
Thanks.
-Nitin
2004 Dec 20
1
Re: [BioC] limma, FDR, and p.adjust
Mark,
there is a fdr website link via Yoav Benjamini's homepage which is: http://www.math.tau.ac.il/%7Eroee/index.htm
On it you can download an S-Plus function (under the downloads link) which calculates the false discovery rate threshold alpha level using stepup, stepdown, dependence methods etc.
Some changes are required to the plotting code when porting it to R. I removed the
2005 Dec 02
1
Zero-inflated neg.bin. model and pscl package
Dear list,
I'm currently trying to develop a model to assess clam yield potential in a
lagoon. I'm using the zeroinfl function of the pscl package to fit a
Zero-inflated negative binomial model, given the high occurrence of zero
counts.
I don't understand from the sentence in the pscl guide "Zero-inflated count
models are a type of two-component mixture model, with a component