similar to: Error in ma.svd(X, 0, 0) : 0 extent dimensions

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

Dear professors and collegues I need to perform a analysis of dates from a nested experimental design. From "Bioestatical Analysis" of Zar "Bimetry of Sokal" & Rohlf "Design and Analysis of Experiments" of Montgomery I have: Sum (mean(x)_i - mean(x)_T)2 / (a-1) -> var(epsilon) + n sigma2_B + n b (sum alfa_i)2 / (a-1) Sum (mean(x)_ij - mean(x)_i)2 /

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

Dear R-users: I am using the package MAANOVA to analyze microarray data and have encountered problems when trying to plot data. I have tried emailing a MAANOVA discussion group, as well as the author of the package, and have not yet received a response so I am hoping that someone on this listserv can be of assistance. There are several functions in MAANOVA (riplot, resiplot) which call the

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 *

Hi, I'm building Tukey's table using qtukey function. It happens that I can't get the values of Tukey's one degree of freedom and also wanted to eliminate the first column. The program is: Trat <- c(1:30) # number of treatments gl <- c(1:30, 40, 60, 120) # degree freedom tukval <- matrix(0, nr=length(gl), nc=length(Trat)) for(i in

Hi all, I'm working with a dataset from 10 treatments, each treatment with 30 subjects, each subject measured 5 times. The plot of the dataset suggests that a 3-parameter logistic could be a reasonable function to describe the data. When I try to fit the model using gnls I got the message 'Step halving factor reduced below minimum in NLS step'. I´m using as the initial values of the

Hi, I used the commands below to make Hartley's table, but some values are NA. require(SuppDists) trat = seq(2, 15, 1) gl = seq(2, 40, 1) har = matrix(0, nr=length(gl), nc=length(trat)) for(i in 1:length(gl)) for(j in 1:length(trat)) har[i,j] <- qmaxFratio(.95, df=gl[i], k=trat[j]) rownames(har) <- gl colnames(har) <- trat head(har) The output (head): 2

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,

I'm new using R im trying to do a tukey test, but when i see the results the p value results in NA im guessing its because i have missing values but im not sure how to fix it AnovaModel.2 <- aov(area ~ trat, data=apilados) > summary(AnovaModel.2) Df Sum Sq Mean Sq F value Pr(>F) trat 4 11847 2961.76 9.9905 1.500e-06 *** Residuals 76 22531 296.46

Hi, I try to plot bars with different colours in a barchart graphic. My idea is make that all X-Levels from trat var with different colour (grey scale). I search for a solution but dont find any. Any help? Thanks dados <- structure(list(Medias = c(0.994169096209855, 0.99416342412449, 0.974683544303797, 0.954430379746835, 0.669047619047619, 0.999999998475569, 0.994163424124514,

Hi, I did the analysis of variance of a split-plot and the effect of treatment was significant. I would like compare treatment means using Tukey. I can't extract the mean square to apply HSD.test to use in agricolae package. anava = aov(ganhos ~ Blocos + Trat*Supl + Error(Blocos/Trat)) names(anava) summary(anava) require(agricolae) HSD.test(ganhos, Trat, df, MSerror, alpha = 0.05)

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

Hi, How I could improve this graphic? http://www.divshare.com/download/10754700-f81 I would like to write groups labels in each panel and override the labels from object. I am try this code: xyplot(percentagem.mortos~tempo|trat, data=bio.ens, type="a", ? ? ? auto.key=list(points=FALSE, lines=TRUE, columns=3), ? ? ? ylim=c(0,100),scales = list(x = list(at = c(48, 72, 96), labels ? ?

Hi R-users I'm trying to do multivariate analysis of variance of a experiment with 3 treatments, 2 variables and 5 replicates. The procedure adopted in SAS is as follow, but I'm having difficulty in to implement the contrasts for comparison of all treatments in R. I have already read manuals and other materials about manova in R, but nothing about specific contrasts were found in them,

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

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 --

Hi: I'm using function lmer from package lme4, and I get this message: " There were 12 warnings (use warnings() to see them)" So I checked them: Warnings 1 to 11 said: 1: optim returned message ERROR: ABNORMAL_TERMINATION_IN_LNSRCH in: "LMEoptimize<-"(`*tmp*`, value = structure(list(maxIter = 50, ... and Warning 12 said: 12: IRLS iterations for glmm did

Buenas, En R, como en la mayoría del software estadístico, no se utiliza ningún nivel de confianza sino que lo que se calcula es el p-valor asociado al contraste. De forma que cuanto más cerca de 0 esté el p-valor "menos credibilidad le damos a la hipótesis nula". Dicho mejor, debemos rechazar la hipótesis nula si el p-valor está por debajo de nuestro nivel de confianza. Por ejemplo,

Hi, I have taken one microarray experiment and trying to implement same statistical measures what they have done.I have taken datasets from GEO platform with accession number GSE1557. In the experiment,about half of double transgenic rats (dTGR) over-expressing the human renin and angiotensinogen genes die by age 7 weeks of terminal heart failure (THF); the other (preterminal) half develops