[BioC] present/absent on 2-color oligo arrays

[Kasper Daniel Hansen]

In my experience, on two color arrays where you have a single probe  
per thing you are measuring, it does not work very well to just say  
"above background". I have data where we had negative controls and  
positive controls and sometimes the positive controls were below the  
negative controls. Granted, we did not have many control probes and  
this array was not run many times, but still.

This might be different for affy style arrays where you have multiple  
different probes measuring the same thing.

Kasper

On Feb 1, 2009, at 11:49 , Naomi Altman wrote:

> Thanks Sam,
> Unfortunately, we do not have an appropriate set of negative  
> controls on the arrays.  We had problems with spike-in controls  
> which we had hoped to use to calibrate
> the arrays.  But it does seem like a good idea.  We are going to  
> compare with the background, which is not ideal but gives us some  
> idea of the situation.
>
> --Naomi
>
> At 08:55 AM 1/31/2009, Samuel Wuest wrote:
>> Hi Naomi,
>>
>> I am doing work on AffyChips, but my samples are from amplified
>> material with inputs from around 500pico - few nanogram range; I  
>> found
>> that the Affy-Algorithmus "MAS5 calls" was not very happy with this
>> type of data and thus compared expression values on the chip with an
>> empirical negative-distribution (background-distribution), please
>> refer to people.brandeis.edu/~dtaylor/Taylor_Papers/BIBE07_PANP.pdf
>> for details (or the Bioconductor-package panp)... I worked on the
>> Arabidopsis chip, and there are "negative" probes on the chip: probes
>> that do not match DNA sequences from newer genome releases anymore...
>> I found that by combining the panp-strategy and the information on
>> negative probes on the chip, I could generate precise and relatively
>> accurate predictions on the expression state of a gene (I can't give
>> you all the details so far).
>>
>> So if there are negative controls/negative probes on the array, you
>> could use them to generate an empirical background-distribution for
>> each array and then compare your other signals to this.... Depends on
>> how many negative probes you'd have... The method works well with the
>> Affy HGU133-series, please refer to the above mentioned sources...
>>
>> Hope this helps??
>>
>> Best, Sam
>>
>> 2009/1/30 Naomi Altman <naomi at stat.psu.edu>:
>> > I have been having an on-going discussion with a colleague about  
>> whether he
>> > can say that some genes are "absent" in some tissues based on two- 
>> color
>> > microarrays - most recently, Agilent arrays.  There are a number  
>> of reasons
>> > that he would like to do this which are a mix of biology and QC.
>> >
>> > He wants to use some (arbitrary) normalized expression level, or
>> > unnormalized level above local background or a percentile of the  
>> whole array
>> > background or ...
>> >
>> > Any suggestions for papers about this?  (We can both think of a  
>> dozen ways
>> > to do it, but without experiments to see if they are valid  
>> methods, or at
>> > least a paper to
>> > cite, I am reluctant to put the statistical seal of approval on  
>> any of
>> > them.)
>> >
>> > Thanks,  Naomi
>> >
>> > p.s. In case anyone thinks that high-throughput sequencing is  
>> going to end
>> > this type of discussion, have a look at the interesting paper by  
>> 't Hoen
>> > comparing sequencing and microarray results.
>> > http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&list_uids=18927111
>> >
>> > 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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>> >
>> >
>>
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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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor