[BioC] limmaGUI: Input files question!

[James Wettenhall]

Marcelo,

The current version of limmaGUI which you have is only designed 
for two-color cDNA arrays, and yes it does assume that you have 
at least these essential columns in the Targets input file: 
SlideNumber, FileName, Cy3 and Cy5
(for Spot, GenePix image analysis files.  May also work for 
QuantArray but haven't really tested these yet.)

For ImaGene image analysis files, the column headings are the 
same except FileName is replaced by two columns, FileNameCy3 and 
FileNameCy5.

Which image analysis software are you using?  

I am working on an affy version of limmaGUI.  I have a 
rough prototype almost working for the estrogen example on the 
Bioconductor site.  But I don't think this will help you...

It sounds like your arrays are cDNA not affy, but they are just 
different to the arrays I've seen in that they don't have two 
dyes.  Maybe you could try something like this:

SlideNumber Cy3 Cy5
1           Ref Control
2           Ref Treated

Then when you look at M values for one slide (not between 
slides), the M value is log2(RedIntensity/GreenIntensity) or 
log2(Cy5Intensity/Cy3Intensity),
so the M values you get for slide 1 in the example above would 
be
log2(Control/Ref)

Does that make sense?  Maybe I'm still not understanding your 
experiment very well.

Regards,
James

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