search for: normalizewithinarrays

...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 message I get is : Read ndd1_1.txt Read ndd1_2.txt Read ndd1_3.txt Error in switch(method, lo...

Dear All, I am facing a problem in calling an user defined R function from Java through JRI. The user defined R function does a loess normalization on micro array data ( find in the limma package of BioConductor) and the last 2 lines of the R Code is : MA <- normalizeWithinArrays(RG, method="loess") return(MA$A) # where MA$A is the column A of MA. Now while calling it in Java, I simply use the following code: String data; data="C:/Project_WRAIR/US09493743_251527910706_1_1 T10-105_5day_24hrs"; //where data is the input. re.eval("source(&...

Can someone show me some code to do normalization by the median of some control genes for the example below? Many Many Thanks in advance This strategy selects a subset of genes (called ?control genes?) and makes the median of their data distribution similar across arrays. ??? ??? id1??? id2??? id3 control1??? 0.8??? 0.7??? 0.6 control2??? 0.6??? 0.2??? 0.4 probe1??? ??? 0.3??? 0.2??? 0.5

...orrected array 18 Warning messages: 1: NaNs produced in: log(x) 2: NaNs produced in: log(x) 3: NaNs produced in: log(x) 4: NaNs produced in: log(x) > w<-modifyWeights(RG$weights,RG$genes$Status,c("rice","beta-actin","18S","GAPDH"),c(0.1,2,2,2)) MA.p<-normalizeWithinArrays(RG.b,weights=w,iterations=6) > design<-modelMatrix(targets,ref="PLAIN") Found unique target names: plain PLAIN plateau PLATEAU > design plain plateau PLATEAU [1,] 0 0 1 [2,] 0 0 1 [3,] 0 0 1 [4,] 0 0 1 [5...