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

[Naomi Altman]

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