Displaying 4 results from an estimated 4 matches for "normalizewithinarrays".
2006 May 25
1
Question regarding reading arrayvision files in limma
...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$P.Value,breaks=50);
The error message I get is :
Read ndd1_1.txt
Read ndd1_2.txt
Read ndd1_3.txt
Error in switch(method, lo...
2011 Oct 24
0
Problem with calling an user defined R function from Java
Dear All,
I am facing a problem in calling an user defined R function from Java
through JRI. The user defined R function does a loess normalization on micro
array data ( find in the limma package of BioConductor) and the last 2 lines
of the R Code is :
MA <- normalizeWithinArrays(RG, method="loess")
return(MA$A) # where MA$A is the column A of MA.
Now while calling it in Java, I simply use the following code:
String data;
data="C:/Project_WRAIR/US09493743_251527910706_1_1 T10-105_5day_24hrs";
//where data is the input.
re.eval("source(&...
2012 Aug 23
3
Please help....normalization by the median of some control genes
Can someone show me some code to do normalization by the median of some control genes for the example below?
Many Many Thanks in advance
This strategy selects a subset of genes (called ?control genes?) and makes the median of their data distribution similar across arrays.
??? ??? id1??? id2??? id3
control1??? 0.8??? 0.7??? 0.6
control2??? 0.6??? 0.2??? 0.4
probe1??? ??? 0.3??? 0.2??? 0.5
2007 Jul 30
0
problems in limma
...orrected array 18
Warning messages:
1: NaNs produced in: log(x)
2: NaNs produced in: log(x)
3: NaNs produced in: log(x)
4: NaNs produced in: log(x)
> w<-modifyWeights(RG$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...