[BioC] ANCOVA microarray time-course continuous & categorical variables / Limma extensions

[Richard Friedman]

On Oct 22, 2013, at 5:30 PM, Michael Breen wrote:

> Hi all,
> 
> Our lab analyzes gene-expression from microarray and RNAseq platforms.
> Currently, I am looking for a package to test differential expression (DE)
> while considering continuous variables that may alter gene-expression
> profiles. In other words, an ANCOVA type tool. I am quite familiar with
> Limma (ANOVA) but including continuous variables is not very well described.
> 
> Specifically, we have a project were two groups can be modeled over the
> same 2 time points. One group starts healthy and ends in a disease state.
> The other group starts healthy and remains healthy.
> 
> We are interested in identifying genes uniquely responding within one group
> and not in the other. Thus, we have implemented a longitudinal contrast
> with linear modeling through Limma. However, we are also interested in
> adding one or two continuous variables (tumor size, time spent meditating,
> the amount of drinks one consumes etc..)  to check if gene expression
> differences or similarities may be due to these factors instead of due to
> belonging to a certain class. Limma seems to test categorical variables,
> but I don't think it is capable of either correlating gene-expression to
> continuous variables.
> 
> If not, can someone recommend  a tool which may be appropriate for such a
> situation?
> 
> Yours,
> 
> Michael
> 
> 	[[alternative HTML version deleted]]
> 
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Dear Michael and list,

	I think that you write the design and contrast matrices
exactly as you would for an ANCOVA in R only you do the
fit and Bayesian correction in Limma. 

Perhaps someone who has had experience doing this 
kind of analysis can comment.

Best wishes,
Rich

Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)/
Columbia Department of Systems Biology
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In memoriam, Frederik Pohl