[BioC] What's the meaning of "covar" in the widget of ReadAffy and how to determine this value?

[James W. MacDonald]

Elaine yang wrote:
> Hi there, I am new in using package and some basic questions for
> ReadAffy. I tried to use ReadAffy(widget=TRUE) function to select the
> cel files by using widget tools. But after I select all the cel
> files, it goes to create the phenodata step. What's the meaning of
> "covar" and how to choose the value of covariate?

The covariate is a descriptive term used to distinguish one sample from 
another. For instance, let's say you have an experiment where you are 
comparing rat liver tumors vs normal liver after treatment with a 
chemotherapeutic agent. You would have (at least) two covariate names 
here. An example of what the covariates would look like is this:

Sample	Treatment	Type
1	Chemo		Tumor
2	Chemo		Normal
3	None		Tumor
4	None		Normal

Does that help?

Best,

Jim


> 
> Thanks in advance!
> 
> Elaine
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
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