 

 

From: Afsaneh [mailto:s.maleki-dizaji@dcs.shef.ac.uk] 
Sent: 15 April 2008 11:23
To: 'wettenhall@wehi.edu.au'
Subject: limma for 2 color data

 

Dear James,

I  was trying to use limmaPackge, 

 

Here is my description file, at the moment I have got only one experiment.


SlideNumber

FileNameCy5

FileNameCy3

Cy3

Cy5


1

Imagene2.txt

Inagene1.txt

Wt

Mutant

					

 

The problem is after normalization when I try to run

fit = lmFit(MA,design= c(1))     ok

 

> topTable(fit)

Error in dim(data) <- dim : attempt to set an attribute on NULL

 

efit <- eBayes(fit)  ??   

 

Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
stdev.coef.lim) : 

  No residual degrees of freedom in linear model fits

 

  

  tops = topTable(efit,coef=1,adjust='fdr',sort.by='B',number = 50000)

 

 

 

I would really appreciate if let me know what is the problem.

 

Best

Afsaneh

 

 

 

 

 

 

 

 

 

 

 

 

 

Here is the code I have used to load and normalize

library(Biobase)

library(vsn)

library(limma) 

library(genefilter) 

library(arrayMagic)

 

setwd("C:/SUMO biological data/ecoli matt exp 1")

 

fileName <- "exp1.txt"

 

 

 

description <- readpDataSlides(fileName)

 

 

files = description$fileName

 

# loading data based on description info file

RG = read.imagene(files = files)

 

RG2 = read.maimage(files,source = "imagene")

 

#Normalization 

RG.norm=backgroundCorrect(RG)

RG.normlg=normalizeWithinArrays(RG.norm,method="loess")

 

RG.norml=normalizeWithinArrays(RG.norm)

 

summary(RG$R)

MA = normalizeWithinArrays(RG, method="none")

MA.l <- normalizeWBetweenArrays(MA)

 

 


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