[BioC] 2 color data...

Naomi Altman naomi at stat.psu.edu
Wed Jul 19 15:31:18 CEST 2006

I would not delete data that is below background, even in both 
channels, if it is above background on at least one array.

It seems to me that it is important information to know that a gene 
does not express under some condition in your experiment.  Of course, 
the unfortunate side-effect of our liking to use ratios is that 
"zero" is not handled well.  But a gene that expresses in some 
conditions of interest but not in others surely is of primary 
interest to your study.


At 11:48 AM 7/18/2006, milesg at bu.edu wrote:
>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? Perhaps 
>there is a way
>to specify to bioconductor that this is the case (by entering a background
>value) and allowing it to handle the data abstractly? Or is it best to let
>Bioconductor look at them as NA's. Any help would be greatly appreciated.
>-Greg Miles
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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