[BioC] 2 color data...

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Wed Jul 19 15:41:05 CEST 2006

Quoting milesg at bu.edu:

> HI, my name is Gregory Miles. I'm at Boston University and was given this
> address by Dr. Carey (I went to a seminar of his last week) at the Harvard
> medical school and was told that I could ask my question about 2 
> color data to
> you. On the mouse microarray dataset we have, there are two colors, and
> therefore two values that can be below background. When both values are above
> background (zero_barcode on our chip), we keep the data and when both are
> below we eliminate the data (they become NA). I imagine this is a correct
> approach, but what should be done regarding the data that has one intensity
> below background and one above. Would it be best to keep the good 
> value? Do we
> eliminate the entire gene from entry into bioconductor?

If you eliminate a gene because it has no signal in one channel, you 
may be eliminating some of the most interesting genes! It depends on 
the biology of your experiments. You should always think about the 
experiment underneath, not just about numbers :-)

A gene with no signal in one channel, but ok signal on the other, may 
be a gene that becomes silenced after your treatment, or switched on. 
In my particular case *those* are the genes that I am after, so I keep 
them and cherish them ;-)

However, when there's no signal in both channels, on all your 
experiments, it sounds reasonable to eliminate them.


Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR

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