[BioC] single channel in limma...

Gordon Smyth smyth at wehi.edu.au
Tue May 25 04:43:33 CEST 2004

At Sat May 15 22:52:19 CEST 2004, Mayte Suarez-Farinas wrote:
>I am trying to use Single Channel Analysis of Two-Color
>Microarrays using limma. This topic is briefly discussed in limmaGui

There is definitely no mention of single channel analysis in limmaGUI. I 
suspect that you are thinking of limma itself.

>and I have some dificulties using intraspotCorrelation. Could somebody
>give me an example that help me to understand what is the design matrix to
>be used in intraspotCorrelation (the description of this matrix in the
>intraspotCorrelation help does not agree with the error message
>about the dimension of design matrix), or some reference....

This is a documentation bug. I have fixed it in limma 1.6.10 available from 
http://bioinf.wehi.edu.au/limma, and have also added an example to the help 
page for lmscFit().

But please note, the single channel analysis code in limma is new and is 
still considered experimental. The fact that the documentation is very 
light is deliberate. You should only use it if you know what you're doing. 
If you're not sure of the difference between limmaGUI and limma, it might 
not be right for you.

Best wishes

>Thanks in advance
>Mayte Suarez Farinas
>The Rockefeller University
>1230 York Avenue, Box 212
>New York, NY 10021
>phone: 1-212-327-8186
>fax:   1-212-327-7422

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