similar to: 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,

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.madata("rmaexpr.dat", designfile = "design.dat") : Assume that

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 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 am trying to use lme to fit a mixed effects model to get the same results as when using the following SAS code: proc mixed; class refseqid probeid probeno end; model expression=end logpgc / ddfm=satterth; random probeno probeid / subject=refseqid type=cs; lsmeans end / diff cl; run; There are 3 genes (refseqid) which is the large grouping factor, with 2 probeids nested within each refseqid,

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 *

I'm working with snow and created a local cluster. So far, the same code has always worked (please see below). However, now I receive a message that the connection with the nodes cannot be opened. I restarted my workstation but that didn't help. Is there a known solution for this problem? Thanks a lot for any help. bram foubert library(snow) cl =

I am trying to use lme to fit a mixed effects model to get the same results as when using the following SAS code: proc mixed; class refseqid probeid probeno end; model expression=end logpgc / ddfm=satterth; random probeno probeid / subject=refseqid type=cs; lsmeans end / diff cl; run; There are 3 genes (refseqid) which is the large grouping factor, with 2 probeids nested within each refseqid,

Full_Name: Henrik Bengtsson Version: 1.5.1 OS: WinMe Submission from: (NULL) (217.210.0.243) In the Perl script $R_HOME/bin/check there is a bug under the section "Check R code for syntax errors" where the 'Rfiles <- c(...)' is build up. If there are too many files in @Rfiles the source code line generated will be too long and weird things will happen, e.g. strange

Hi Everyone, Thanks for all the help with the previous queries. Here is what i want to do. i have 20000 probesets-->calculate all the variance accross all the probesets-->filter out probesets that are low so now i ended up with only 10000. The 10000 is fine but when i export to excel, it is missing the probeID. Here are my code and examples. #########calculate the variance across the

When doing repeated regressions on large data sets, I'm finding that the time spent on garbage collection often exceeds the time spent on the regression itself. Consider this test program which I'm running on an Intel Haswell i7-4470 processor under Linux 3.13 using R 3.1.2 compiled with ICPC 14.1: nate at haswell:~$ cat > gc.R library(speedglm) createData <- function(n) {

Hello, Thanks everyone for helping me with the previous queries. step 1: Here is the orginal data: short sample ProbeID Sample_1_D Sample_1_C Sample_2_D Sample_2_C 1 224588_at 2.425509867 11.34031409 11.46868531 11.75741478 step 2: i calculate the variance of the sample using this R code x<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y])#create data.matrix

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

On Wed, 14 Aug 2002, Henrik Bengtsson wrote: > Sorry, but it was indeed the redirection of the standard output in > Cygwin/bash that cause the first problem, not R (I should stop doing > troubleshooting at 1:00 AM). So please forget about the problems reported in > R_CMD_check.out. However, it would still be nice if you still update R CMD > check to do join with "\n".

This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ------=_NextPart_000_0006_01C2432C.7ACD6BA0 Content-Type: TEXT/PLAIN; CHARSET=iso-8859-1 Content-Transfer-Encoding: 8BIT Content-ID: <Pine.GSO.4.44.0208140920312.15226@auk.stats>

Here is my R Code x<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y])#create data.matrix variableprobe<-apply(data.matrix[x,],1,var) variableprobe #output variance across probesets hist(variableprobe) #displaying histogram of variableprobe write.table(cbind(data[1], Variance=apply(data[,y],1,var)),file='c://variance.csv') #export as a .csv file. Output in Excel all in 1

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

Hi, I am interested in using the cast function in R to perform some aggregation. I did once manage to get it working, but have now forgotten how I did this. So here is my dilemma. I have several thousands of probes (about 180,000) corresponding to each gene; what I'd like to do is obtain is a frequency count of the various occurrences of each probes for each gene. The data would look

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

I have a file with a data in columnar format like below: probeID rc_AI104113_at rc_AI178259_f_at rc_AI179134_i_at rc_AI179134_f_at rc_AI104113_at rc_AA819429_f_at How can I rewrite it in the format below: 'rc_AI104113_at', 'rc_AI178259_f_at', 'rc_AI179134_i_at', 'rc_AI179134_f_at', 'rc_AI104113_at', 'rc_AA819429_f_at' Is there any function to do