search for: maanova

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 fu...

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 * checking whether 'INDEX' is up-to-date ... NO * use '...

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...

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...

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 ca...

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 St...

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 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...

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...

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 from La.svd() if the data object is big. Error...

...4 week-old male untreated dTGR.Untreated dTGR were divided in two subgroups, rats with cardiac hypertrophy (n=18) and rats with THF (n=8).Rats were killed at age 7 weeks.Total RNAs (five animals per group) were isolated from the left ventricle.For all rgu34_a affymetrix chips were used. Iam using maanova package. In using fitmaanova function, we have to set variables to formula and random.Plz, suggest me what to take in formula and random. *fit.fix <- fitmaanova(rat, formula = ~Array+sample, random = ~Array)* Error in fitmaanova(rat, formula = ~Array + sample, random = ~Array) : Not enough de...

Hi, Am using maanova package for doing anova.But am getting error like this..plz, help me regarding this.. > TGR=read.madata("rmaexpr.dat",designfile="design.dat") Reading one color array. Otherwise change arrayType='twoColor' then read the data again Warning messages: 1: In read.madat...

Hello, unfortunately I have I big problem I can't solve. I have to analyse if a gene is tissue specific. For example for the gene xyz I have following expression values: Heart Liver Brain 8.998497 10.013561 12.277407 9.743556 10.137574 11.033957 For every tissue I have two values from two different experiments. Now I want to test if Heart is significant higher

Hi all, I am having memory allocation problem with my R 2.2.1 for Mac OS. The following is the error message that I get. I do not get this message if I break down the large dataset in to sub datasets. I think breaking up the dataset is not a sustainable solution in the long run. The data that I am analysing is essentially big, and it would be reasonable to do the analyis on the whole dataset

Hi, I'm trying to fit a model using variance components in R, but if very new on it, so I'm asking for your help. I have imported the SPSS database onto R, but I don't know how to convert the commands... the SPSS commands I'm trying to convert are: VARCOMP RATING BY CHAIN SECTOR RESP ASPECT ITEM /RANDOM = CHAIN SECTOR RESP ASPECT ITEM /METHOD = MINQUE (1) /DESIGN

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I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

...fit","lodplot","LogicReg","logistf","logspline","lokern","longitudinal","longmemo","LoopAnalyst","LowRankQP","lpridge","lpSolve","lsa","lspls","ltm","maanova","magic","mapLD","mapproj","maps","maptools","maptree","mAr","marg","MarkedPointProcess","MASS","Matching","MatchIt","mathgraph","matlab","Matrix&quo...

Hi, Thanks for reading. I am running a process in R for microarray data analysis. RedHat Enterprise Linux 4, dual AMD CPU, 6G memory. However, the R process use only a total of <200M memory. And the CPU usage is total to ~110% for two. The program takes at least 2 weeks to run at the current speed. Is there some way we can increase the usage of CPUs and memories and speed up? Any

...tentnet (2.3-0), lattice (0.18-8), latticedl (1.1), latticeExtra (0.6-11), latticist (0.9-43), lda (1.2.1), ldDesign (1.2-0), lemma (1.3-1), lgtdl (1.1.1), limSolve (1.5.2), linprog (0.9-0), lme4 (0.999375-34), logging (0.4-42), logistf (1.10), longitudinalData (0.6.5), lordif (0.1-5), ltm (0.9-4), maanova (1.18.0), MAc (1.1), MAd (0.8), mapdata (2.1-3), maps (2.1-4), maptools (0.7-34), marelac (2.1), MASS (7.3-7), Matrix (0.999375-42), matrixStats (0.2.1), maxLik (0.7-2), mbmdr (2.1), mboost (2.0-6), mc2d (0.1-8), mclust (3.4.4), mcmc (0.8), mco (1.0.9), mecdf (0.4.1), memisc (0.95-30), meta (1.6-0)...