search for: genepix

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 pack...

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 d...

...r 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 Candidate) The Australian National University School of Biochemistry and Molecular Biology Linneaus way, building 41 Canberra, ACT 0200 Australia email: bart.rossel@anu.edu.au phone: +61 02 61252663 FAX: +61 02 6...

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seems to have something to do with the format of my files

...ally 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 file","*.gpr"), nc=2, byrow=T)) The popup browse window is first displayed and once I've selected my files the cat "IMPORT..." is displayed. What can I do to make my displays appear at the right time? Thanks a lot. Laetitia Marisa.

Hello, I have some files generated from microarray experiments. I used scan() to read the files, and assigned each file to a unique name with many rows and columns. Now I want to create a array (ArrayA) with unique names, and I can use ArrayA[1,2][[6]] to refer the data in each file. Is there any packages available for array of array? Thanks! [[alternative HTML version deleted]]

...in controls. Here is the code: library(limma) library(RColorBrewer) library(vsn) Cy5 <- "F635 Mean" Cy5b <- "B635 Mean" targets <- readTargets("targets.txt") #My gpr files do only contain 1 channel (Cy5) RG <- read.maimages( targets$FileName,source="genepix",columns=list(R=Cy5,G=Cy5, Rb=Cy5b, Gb=Cy5b)) RG$G <- NULL RG$Gb <- NULL RG$genes <- readGAL("array_human_mirs.gal") #Here are my spike in controls for normalization isSpikeIn <- grep("CTL", RG$genes$Name) #The vsn normalization works fine mat <- vsnMatrix(...

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

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

...PLATEAU Locust 198.gpr 2006-6-8 14 plateau PLATEAU Locust 199.gpr 2006-6-8 15 plateau PLATEAU Locust 200.gpr 2006-6-8 16 plateau PLATEAU Locust 201.gpr 2006-6-8 17 plateau PLATEAU Locust 202.gpr 2006-6-8 18 plateau PLATEAU Locust 203.gpr 2006-6-8 > RG<-read.maimages(targets,source="genepix",wt.fun=wtflags(0.1)) Read Locust 186.gpr Read Locust 187.gpr Read Locust 188.gpr Read Locust 189.gpr Read Locust 190.gpr Read Locust 191.gpr Read Locust 192.gpr Read Locust 193.gpr Read Locust 194.gpr Read Locust 195.gpr Read Locust 196.gpr Read Locust 197.gpr Read Locust 198.gpr Read Locust...

I have just spent a day trying to determine why I seemed to be unable to read a file of microarray expression results into R properly. The file was produced by the Dchip software developed by Li and Wong at Harvard's Department of Biostatistics. It contains rows of tab-delimited fields in the order Probe set identifier Probe set description Array 1 expression Array 1 call Array 2 expression