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Hi BioC user, I have a problem extracting the gene set I would like to work with. Here is I work with my data: normData <- read.delim("normalizedData.txt",sep ="\t") ######### two class unpaired comparison # y must take values 1,2 classes <- c(-1,-2,1,2) #prepere the data for the samr analysis data.x <-as.matrix(normData[,8:11]) d=list(x=data.x,y=classes,

Hi, I have a problem on my mac when trying in R to produce png images. I am getting this warnings with the ArrayQualityMetrics package: > arrayQualityMetrics(rma_fatBody, outdir="normData", force =T) The report will be written into directory 'normData'. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) libpng warning: Application built

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

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

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

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

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.05 which is quite conservative (i.e., very

I try to send this message To Gordon Smyth at smyth at vehi,edu.au but it bounced back, so here it is to r-help I am trying to use limma, just downloaded it from CRAN. I use R 2.0.1 on Win XP see the following: > library(RODBC) > chan1 <- odbcConnectExcel("D:/Data/mgc/Chips/Chips4.xls") > dd <- sqlFetch(chan1,"Raw") # all data 12000 > # > nzw <-

Hi all. I've got a really dumb question for anyone. How do I write the output of a limma analysis (basically the topTable) to a text file? I want to output the topTable for the entire microarray (not really a topTable anymore I suppose..). Thanks for any advice! -Josh

Hi, I am relatively new to R and Bioconductor and am trying to filter the topTable that I generated of differentially expressed genes from my normlized eset file comprised of ~ 40 HG-133A Affy microarrays . I would like to see if particular probesets are represented in this list. Alternatively I would like to generate a topTable of differentially expressed genes using only specified probesets

Hello, I have just completed an analysis of microarray data using the limma package. The analysis appears to have worked fine. However, when I use the topTable function to get the significant genes, I get the following error: > topTable(fit2,coef=5,adjust="fdr") Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x), : attempt to set an attribute on NULL

On Wed, December 22, 2004 12:11 am, r.ghezzo at staff.mcgill.ca said: > ----- Forwarded message from r.ghezzo at staff.mcgill.ca ----- > Date: Mon, 20 Dec 2004 15:45:11 -0500 > From: r.ghezzo at staff.mcgill.ca > Reply-To: r.ghezzo at staff.mcgill.ca > Subject: [R] problems with limma > To: r-help at stat.math.ethz.ch > > I try to send this message To Gordon

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

Hallo, > fit12<-lmFit(qrg[,1:2]) > t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1]) > t12 ID logFC t P.Value adj.P.Val B 522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965 1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520 1.944046 Can anyone tell me what the difference is between P.Value

I have the following code, from which I get the following error message: Error in dim(data) <- dim : attempt to set an attribute on NULL I think the error is coming from the part of my code in BOLD RED. The script works fine until then. #Load libraries source("http://bioconductor.org/biocLite.R") biocLite() library(limma) library(Biobase) #change directory to folder where

Hi R guru coders I wrote a bit of code to add a new column onto a "topTable" dataframe. That is a list of genes processed using the limma package. I used a for loop but I kept feeling there was a better way using a more vector oriented approach. I looked at several commands such as "apply", "by" etc but could not find a good way to do it. I have this feeling there

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

>>>>> "GS" == Gordon K Smyth <smyth@wehi.edu.au> >>>>> on Sat, 8 Jan 2005 01:11:30 +1100 (EST) writes: <.............> GS> p.adjust() unfortunately gives incorrect results when GS> 'p' includes NAs. The results from topTable are GS> correct. topTable() takes care to remove NAs before GS> passing

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