search for: maimag

Displaying 11 results from an estimated 11 matches for "maimag".

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2005 Dec 01
1
maImage() and layout()
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...
2004 Oct 19
1
Error in grep
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...
2011 Jun 07
1
Error message
...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...
2007 Jul 08
2
how to revert to an older limma version?
...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...
2006 Jan 12
4
Loading Excel file into Limma
...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
2011 Apr 09
1
Compression of largish expression array files in the DAAGbio/inst/doc directory?
...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...
2012 May 23
2
File format for single channel analysis of Agilent microarray data in Limma?
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...
2006 May 25
1
Question regarding reading arrayvision files in limma
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...
2009 Mar 13
0
Singal channel spike in controls with custom microRNA slides - Normalization help needed
...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...
2018 Mar 20
0
Problem with lvs Normalization
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
2007 Jul 30
0
problems in limma
...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...