[BioC] 2 color data...

[Sean Davis]

Just to add a bit here, with many image analysis options, there are other
measures of the "quality" of a spot besides intensity.  Since limma will
allow you to incorporate this information into an analysis, you might think
about whether there is some quantity reported by your image analysis
software that might be useful in this regard.

I agree with Naomi that excluding genes based on low-intensity spots in some
subset of the arrays may be discarding some of the most interesting data.

Sean


On 7/19/06 8:10, "Naomi Altman" <naomi at stat.psu.edu> wrote:

> 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
> 
> _______________________________________________
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