[BioC] simple ANOVA

[James MacDonald]

There is a bug in the version of limma that you are using. Update to the
developmental version, and you should be fine.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> "Roger Vallejo" <rvallejo at psu.edu> 11/26/03 2:12 PM >>>
I have a very simple design: it has 2 tissues (saline vs ecoli
injected), 2 time-point evaluation (24 hr and 48 hr post injection) with
2 observations per experimental unit (2 reps). We are using Affymetrix
genechip arrays (mouse expression set 430A), so it makes a total of 8
arrays. It is a very simple ANOVA that I am trying to analyze using the
R-package. I am using a UNIX SunOS 5.8, Solaris 8.0. I have followed the
LIMMA vignette, and I got this error message: "No residual degrees of
freedom in linear model fits". 

These are the commands that I used:

************************************************************************
**************

Limma 11/24/03 (did not work why?):

> The usual: change directory in R-window

> library(affy)

> Data <- ReadAffy()

> Data

> eset <- expresso(Data,bgcorrect.method="rma",
normalize.method="quantiles", pmcorrect.method="pmonly",
summary.method="medianpolish")

> exprs(eset)            ## runs for awhile, 5 minutes for 22K
probesets.

> design <- model.matrix(~ -1+factor(c(1,2,1,2,3,4,3,4)))        ## I
have array1-8 (4 RNAs and 2 reps)

> colnames(design) <- c("group1", "group2", "group3", "group4")  ## I
assume the groups refer to RNAs

> library(limma)

> fit <- lmFit(eset, design)                                 ## works
here

> contrast.matrix <- makeContrasts(group2-group1, group4-group3,
levels=design)

> fit2 <- contrasts.fit(fit, contrast.matrix) 
> fit2 <- eBayes(fit2)                                            ##
here I got error messages "no residual df in model fits"

************************************************************************
*************************************************************

 

I would appreciate having some help on solving this problem.

Thanks a lot.

Roger

 

 

Roger L. Vallejo, Ph.D.

Assist. Professor of Genomics/Bioinformatics

The Pennsylvania State University

Department of Dairy & Animal Science

Genomics & Bioinformatics Laboratory

305 Henning Building

University Park, PA 16802

Phone:        (814) 865-1846 

Fax:            (814) 863-6042

Email:         rvallejo at psu.edu <mailto:rvallejo at psu.edu> 

Website:     http://genomics.cas.psu.edu/ <http://genomics.cas.psu.edu/>


 


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