[BioC] 2 color data...

[Naomi Altman]

I would not do this.  Use less background correction, (e.g. don't 
background correct, or subtract 1/2 of the background), or set the 
channels that are below background to some low value (e.g. 1) so that 
logs can be used.

--Naomi

At 09:48 AM 7/19/2006, you wrote:
>Thanks for your quick response. I will not delete the gene completely (if you
>delete genes then LIMMA doesn't know how to handle genes lists with different
>orders), but although it is helpful to keep genes that may have 
>information in
>one array, I do think it may be necessary to "NA" the below background values
>and keep the above background ones. Thus you still have the good values but
>have eliminated possible bad ones. What do you think of this?
>-greg
>
>Quoting Naomi Altman <naomi at stat.psu.edu>:
>
> > 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.
> >
> > --Naomi
> >
> > 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.
> > >Thanks!
> > >-Greg Miles
> > >
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> >
> > 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
> >
> >

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