[BioC] limmaGUI: Input files question!
James Wettenhall
wettenhall at wehi.edu.au
Mon Oct 20 01:29:36 MEST 2003
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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