similar to: limmaGUI

Full_Name: Edoardo Giacopuzzi Version: 2.0.1 OS: Windows XP Home Submission from: (NULL) (80.181.65.157) I have some problem with this new version of R GUI. I've used limmaGUI package with an older version of R and it works perfectlly, but now with the last version R 2.0.1.0 two error boxs appear every time I try to launch this package: 1. <<Error in list.files(path, pattern,

Hi Everyone, I have been trying to read some Arrayvision files( 2 channel cDNA) and am having some problem. My code is : setwd('C:/work/data/limma/ndd1'); files <- c('ndd1_1.txt','ndd1_2.txt','ndd1_3.txt'); RG=read.maimages(files,"arrayvision",sep="\t"); #Normalisation MA=normalizeWithinArrays(RG); #plotPrintTipLoess(MA); #Fit Linear

Hi. Is it possible to make gpr from raw? library(aroma) #read gpr file gpr <- GenePixData$read("gpr123.gpr", path=aroma$dataPath) # gpr -> raw raw <- as.RawData(gpr) # raw -> ma ma <- getSignal(raw, bgSubtract=FALSE) ma.norm <- clone(ma) #normalization normalizeWithinSlide(ma.norm, "s") #ma -> raw raw2 <- as.RawData(ma) I want to make gpr data from

Dear R users, I'am using marray and Limma packages to analyze genepix output. 1) how can I filter bad spots from my data (data contains 3 types of bad spots). my experiment contains 12 samples and the bad spot are not associated to the same probes 2) how can I remove control probes from my data ? I'm sorry, i'm new with R and I can't find answer in packages doc. best regards,

Hi, I'm working with custom slides(Cy5) and working in the normalization of the arrays. I have three arrays (technical replicates). I have sucesfully normalized the data using vsn, however i would like to normalize using spike in controls. My controls are annotated as CTL-1 to x and i would like to do etiher a normalization by block per array or the mean of all the controls per array. The gal

Hello, In limmaGUI, after running a linear model for a single gene & time point (mutant vs control), the venn-diagram for differentially expressed genes with a p-value cut-off gives a different number than the top-table with the same cut-off (2600 vs. 791). I have seen the same thing happen before for multiple time points (when the venn-diagram is more relevant) Any ideas what is going on?

Dear whom this may concern, I am having problems running R under windows XP. I can source files and get all the functions loaded, but when directing it to a file to carry out analyses it comes up with an error message. I am using R for analyses of gpr files generated from microarray slides using Axon genepix 2000. I hope you have a solution to my problems. Kind regards, Jan Bart Rossel (PhD

Hello, When I launch a script under windows it does not display sequentially my cat calls or maybe the console is not refreshed at every line of my script. For instance with that code cat("\n\n================== IMPORT DATA FROM FILE ===================\n\n") fileschosen <- choose.files(caption="Select gpr files", filters = matrix(c("genepix

Full_Name: Bart Version: 1.7.1 OS: XP Submission from: (NULL) (150.203.41.62) When trying to load microarray slides (gpr format) into R 1.7.1, I get the following error message Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1057 did not have 43 elements I have been able to load the files on another computer before including an XP machine. I have

Dear list members, I am analysing my microarray data using limma package. Now I encounter several problems. Looking forward to your suggestions! Question 1: During the process of background correction using method="normexp", four warning messages appeared as "NaNs produced in: log(x)" (as you can see in the program posted below). What does that mean? How will it effect the

I would like to load ApoAI.RData. During the operation of reading this data an error occurs. There is also a problem with STF file. > library (limma) > load("ApoAI.RData") Warning message: 'RG' looks like a pre-2.4.0 S4 object: please recreate it > objects() [1] "RG" > names(RG) [1] "R" "G" "Rb"

Hello, I am not only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the channel of interest eg. Cy5 or Cy3 across the set of experiments). I might have missed a straight forward

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Hi, I am wirting a R script to process some data routinely and have a problem when try to get the content of object in ls()? Here is the script: > ls() [1] "a" "b" [3] "files.num" "fll92_1a_gpr" [5] "fll92_1a_gpr_norm" "fll92_1a.gpr.norm.scale" [7] "fname" "fullnames" [9] "gal" "galfile" [11]

Could anyone please explain to me why the following writes nothing into "all.Rout" file? If the "for" loop is removed, t.test output can be written into "all.out". Thanks in advance. Minghua Yao ...... zz <- file("all.Rout", open="wt") sink(zz) for(i in 1:n) { Cy3<-X[,2*i-1]; Cy5<-X[,2*i]; t.test(Cy3, Cy5)

[PLEASE REPLY _OFF_ THE LIST, i.e. DON'T CC to r-help at ...] Hi, I don't see this sort of thing very often on the mailing lists, so list moderators and others should feel free to tell me if it breaches list etiquette and/or delete my post if necessary. But I can't see what harm it could do... I am just wondering approximately how many people use / have used some of the R stuff

Dear R user! I have a small question! I have calculated the relative importance of the variables. However I would like to compare the relative importance of two different groups of variables (i.e Strategy and industry) For example let me say that strategy has 2 sub varialbes and industry has four different variables! Can I simply add the importance of those four industry variables importance

Hi, I'm using rw2000dev.exe (Win32) built on August 14. If this isn't already planned, can I suggest that when checkS3methods() (called by R CMD check) fails because of a syntax error in a dependent package listed in the DESCRIPTION file of the main package being checked, it would be nice if checkS3methods() reported which dependent package caused it to fail? Running R CMD check on my

Hi all, I'm working on microarray and currently analyzing the microrarray data using limmaGUI. Loop design has been applied in this experiment. This is a 2X2 factorial experiment where there are control and treatment at 2 different time points, week 6 and 9. The experimental design is almost the same as the limmaGUI work example: Weaver Data set. I would like to look at the effect of

Hi, I have some microarray data, cy5 and cy3 values are in log2. Is there a way to check they have undergone lowess normalization ? Thanks Stanley [[alternative HTML version deleted]]