Displaying 20 results from an estimated 700 matches similar to: "Using MAANOVA functions"
2004 Dec 07
1
Importing module into R library
Hello,
I am basically familiar with R and am trying to import a module that someone
else has written. I know that it must go into the R library but even after
I place the file there R doesn't recognize it. The module is maanova,
available from the Churchill lab group for analysis of microarray data, if
anyone is familiar with it. Any ideas/help?
Thanks,
Heather
--
2004 Dec 31
3
Citation
Does anyone know R is to be cited in a publication? I've looked everywhere
on the website and cannot find this.
Thanks,
Heather
--
Heather Maughan
Department of Ecology and Evolutionary Biology
Biosciences West 310
University of Arizona
Tucson, AZ 85701
Phone: 520-626-5108
Fax: 520-621-9190
hmaughan at u.arizona.edu
2005 Feb 17
2
Extracting values from linear models
Hello:
I want to use values from the output of linear models done using permuted
data to construct a random distribution. The problem I am having is the
extraction of a value, say the p-value or the regression coefficient, from
the summary of a linear model. When summarizing a linear model I get this:
Call:
lm(formula = fitness ~ mm)
Residuals:
Min 1Q Median 3Q Max
2006 Nov 13
2
Forcing the intercept
Dear R-users:
I am doing multiple regressions using the "lm" function and would like to
force the intercept to be equal to a specific value (such as 4.3). I was
able to find out how to force it through the origin but this does not work
for other values.
I am also interested in forcing the regression parameters obtained from one
regression in another regression with a subset of the
2007 Nov 13
0
Difficult to set a quiet formula in maanova
Hi,
I am trying to run an analysis with the package maanova and I am not
getting success.
I suppose that I am wrong on set up the formula, so the issue may not
be related to R, properly.
I have two varieties of plants (V1 and V2). A group of each ones were
treated and another was not treated. After treatment, in three
different time RNA was collected from treated and from not treated
plants for
2004 Jan 05
1
install on windows
I'm trying to install packages on windows XP and I have trouble with
command Rcmd build (R version 1.8.1) :
In the Windows console for package maanova for example, answer is :
C:\Documents and Settings\dillies\Mes documents\ghis\packages>Rcmd
build maanova
* checking for file 'maanova/DESCRIPTION' ... OK
* preparing 'maanova':
* cleaning src
*
2010 Jul 06
2
Could not find createData function
Hi,
I am using "*Maanova* package" to do anova. I have created *datafile* with
probeID as the first column, which is a tab limited text file and also
created *designfile*. I have created *readma object* which is named as abf1.
>From that readma object, i have to create data object by using
*createData*function and also i hav to create model object by using
*makemodel* function,
2008 Feb 23
1
Error in ma.svd(X, 0, 0) : 0 extent dimensions
Hi,
I run a maanova analysis and found this message error:
Error in ma.svd(X, 0, 0) : 0 extent dimensions
I did a google search and found this:
\item ma.svd: function to compute the sigular-value decomposition
of a rectangular matrix by using LAPACK routines DEGSVD AND ZGESVD.
\item fdr: function to calculate the adjusted P values for FDR control.
I did a search for LAPACK and
2003 Jul 06
1
Printing multiple graphics devices
Hi
I'm using a function (arrayview from the maanova package) that produces
12 plots, all in separate windows. How can I get each one to print to a
jpeg file as the plots are produced? Alternatively, is it possible to
get dev.print (jpeg.....) to print all open graphics devices to separate
windows?
Thanks in advance,
Nat Street
--
Nathaniel Street
University of Southampton
2008 Feb 26
0
Help needed to analyse a factorial microarray experiments! Newbie Question
Dear R-users:
I am using the package MAANOVA to analyze microarray data and have
encountered problems when trying to get interactions.
I am a newbie in both, R and maanova, and I do not have good knowledge in
statistical methods.
I have four effects:
Effects Levels
Var 2
Ind 2
Trat 2
Time 4
Sample 3 <-- biological replicate
Spot 4 <-- technical replicate
I had
2010 Jul 06
0
Error in createData function
Hi,
I am using "*Maanova* package" to do anova. I have created *datafile* with
probeID as the first column, which is a tab limited text file and also
created *designfile*. I have created *readma object* which is named as abf1.
>From that readma object, i have to create data object by using
*createData*function and also i hav to create model object by using
*makemodel* function,
2002 Nov 01
1
init.data function error
We had been using R1.2.3 "print tip lowess function" as described by
Terry Speed's group to normalize microarray data and up until this week
the commands we were using were working fine.
First, we load our data using arrayname<-read.table("filename",
header=T)
and then check that the table is OK.
We format the data list using setup1<-init.data() and usually get a
2006 Jan 10
2
standardized residuals (rstandard & plot.lm) (PR#8468)
This bug is not quite fixed - the example from my original report now =
works using R-2.2.1, but
plot(Uniform, 6)
does not. The bug is due to
if (show[6]) {
ymx <- max(cook, na.rm =3D TRUE) * 1.025
g <- hatval/(1 - hatval) # Potential division by zero here #
plot(g, cook, xlim =3D c(0, max(g)), ylim =3D c(0, ymx),=20
main =3D main, xlab =3D
2019 Jan 19
4
sieve issue after upgrad
On 19/01/2019 08:01, Aki Tuomi wrote:
>
>> On 19 January 2019 at 02:07 Tim Dickson via dovecot <
>> dovecot at dovecot.org <mailto:dovecot at dovecot.org>> wrote:
>>
>>
>> i recently upgraded a server from dovecot 2.1 to 2.3
>> unfortunately sieve does not appear to be working. The user scripts have
>> not changed, and neither has the
2004 Nov 24
6
Searching for antilog function
Dear R-users,
I have a basic question about how to determine the antilog of a variable.
Say I have some number, x, which is a factor of 2 such that x = 2^y. I
want to figure out what y is, i.e. I am looking for the antilog base 2 of x.
I have found log2 in the Reference Manual. But I am struggling how to
get the antilog of that.
Any help will be appreciated!
> version
platform
2004 Aug 13
3
Question from Newbie on PostScript and Multiple Plots
Hi,
As I'm pretty new to R I hope this question isn't too basic.
I am currently looping through my dataset and for each iteration am
producing three separate plots. When I output these plots to the screen
they are nicely grouped as three plots per page, however, when I try to send
it to a PostScript file I get one page for each plot. I have adjusted my
postscript options so that my
2013 Mar 11
3
Test of Parallel Regression Assumption in R
Hi,
I am running an analysis with an ordinal outcome and I need to run a test
of the parallel regression assumption to determine if ordinal logistic
regression is appropriate. I cannot find a function to conduct such a test.
>From searching various message boards I have seen a few useRs ask this same
question without a definitive answer - and I came across a thread that
indicated there is no
2019 Jan 19
2
sieve issue after upgrad
i recently upgraded a server from dovecot 2.1 to 2.3
unfortunately sieve does not appear to be working. The user scripts have
not changed, and neither has the dovecont config. using managesieve
allows me to create new sieve files and setting one as default updates
the link in ~/ to point to the correct file, but the .dovecot.svbin file
is not changed (unless i run sievec
2007 Feb 05
0
strange error message get from La.svd(X)
Generator Microsoft Word 11 (filtered medium) Hi,
I'm the mannova package maintainer. We used La.svd(X, method="dgesvd") in maanova package before. After R-2.3.0, the old La.svd() method was deprecated for option method="dgesvd". I changed maanova code correspondingly, which will call method="dgesdd" instead. But after that, we keep getting below error message
2016 Apr 27
4
polygon angle option perpendicular to axis
I am trying to use the angle option in polygon to create polygons filled with horizontal and vertical lines. The polygons I am crating are irregular and it the angle function appears to set the angle of the shading perpendicular to the polygon sides rather than perpendicular to the axes. Is there any way to set the angle relative to the axes rather than relative to the polygon sides?