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Dear all, Trying to produce 4 maImage plots (marray package) on the same device (2 on the top and 2 on the bottom) with the layout() function or the split.screen() function, we are facing the following problem: it seems that maImage() does nt care about any of these 2 functions, and plots only one image at a time. Maybe this is inher...

Hi, there. I used the function read.maimages in limma package to analyze the microarray data .but I got following message >RG <- read.maimages(targets$FileName, source="spot") Error in grep(pattern, x, ignore.case, extended, value, fixed) : invalid argument I don't know what is the matter Thanks a lot Regards...

...07_Sep09_1_1_32914.txt" [2] "./GSM696981_US81503234_252741110209_S01_CGH_107_Sep09_1_2_32916.txt" [3] "./GSM696982_US81503234_252741110209_S01_CGH_107_Sep09_1_3_33021.txt" [4] "./GSM696983_US81503234_252741110209_S01_CGH_107_Sep09_1_4_33024.txt" > RG <- read.maimages(fn,source="agilent",quote="",other=c("gProcessedSignal","rProcessedSignal","gProcessedSigError","rProcessedSigError"), + columns=list(G = "gMeanSignal",Gb = "gBGMedianSignal", R ="rMeanSignal", Rb = "rB...

...r limma version? Typing "install.packages("limma")" in R gives a list of mirrors. How can I install the version I want after I obtain and untar the file (e.g, limma_2.9.1.tar.gz)? I am running R 2.5.0 on a Linux machine (CentOS 5). When using limma it will not go past the read.maimages command. I get this error: Error in readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file In addition: Warning message: input string 1 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) I was t...

...mand, but it cannot open the file. I renamed the file as .R and .RData, to no avail. The Excel data contains one gene name per row and about 100 data points per gene (columns). I am only used to loading preprepared microarray data with all the t's crossed and i's dotted, with the read.maimages command. Can anyone help me out with this silly-sounding "challenge"? Sincerely - in the truest sense - Norman Goodacre

...ch. It would be useful to be able to zip then, but that as matters stand interferes with the use of the Sweave file that uses them to demonstrate input of expression array data that is in the "spot" format. They do not automatically get unzipped when required. I have checked that read.maimages (in limma) does not, unless I have missed something, have an option for reading zipped files. Is there any way to get around this without substantially complicating the exposition in marray-notes.pdf (also in the inst/doc subdirectory)? John Maindonald email: john.maindonald at anu...

Hi, I am following the protocol outlined here for analysis of single channel Agilent microarray data: http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma I keep getting the following error message when using Limma's read.maimages function to load my data into an RGList object: Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of items to replace is not a multiple of replacement length I think this may be due to my Agilent raw data txt files being in the wrong format. I am having difficulty finding an example A...

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 model and Empirical Bayes method fit=lmFit(MA); fit <- eBayes(fit) ; res=topTable(fit,sort.by="P",number=7200); hist(res$P.Value,breaks=50); The error...

...ray structure. Each block contains spike 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 norm...

Hi! Anyone can help how I can do LVS normalization starting from an EList.raw created using: data= read.maimages(files, green.only=T, columns= list(E='gMedianSignal',Eb='gBGUsed')) thanks in advance

...197.gpr 2006-6-6 13 plateau 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 R...