[BioC] marray and gathering additional information from GenePix GPR file

Jenny Drnevich drnevich at uiuc.edu
Fri Jul 7 20:50:05 CEST 2006

Hi Daniel,

At 10:35 AM 7/7/2006, Daniel Brewer wrote:

>Jenny Drnevich wrote:
> > Hi Daniel,
> >
> >
> > First, I would caution you about discarding all spots called 'bad' by
> > your GenePix setup - do you really know what it's doing? Often, spots
> > are labeled 'bad' if the spot foreground is not detectable above some
> > level of the background. Unless there is a defect on the chip, these
> > type of spots are actually 'real' data, not 'bad' data - more like a
> > value of 0. Now, the number that is associated with that spot is not
> > entirely accurate, but it is relatively accurate compared to spots with
> > detectable values. In an extreme example, by throwing out these spots,
> > you may not detect a gene that is only turned on in one of your
> > treatment groups! However, you do need to discard spot values that are a
> > result of obvious defects on the array, so you still need an answer to
> > your question:
> >
>Thanks for that, that makes a lot of sense.  There are "spots" that are
>empty by design (there is no spot there) and are indicated as such in
>maControls. Is it ok, and sensible to remove these from the object?
> > mraw2 <- mraw2[maControls(mraw2) == 'probes']

Yes, you can remove empty 'spots' because in this case, you are talking 
about removing the same spot on every array, not just particular arrays. 
I'm assuming maControls(mraw2) is a vector with length== #spots per array 
and if so, the proper way to subset to pull out all the rows corresponding 
to 'probes' should be:

mraw2 <- mraw2[maControls(mraw2) == 'probes' , ]

I also want to clarify (for the record) what I meant about spots with '0' 
values - I was referring to the individual channel intensities, not the log 
ratio. If both channels' intensities were 0, then the log ratio would be 
undefined, but in practical terms, the log ratio should be 1 (not changed) 
for undetectable spots. If you are using log ratios for the statistical 
analysis, you might want to check that your undetectable spots are close to 
1 after pre-processing, and if they are not, you might consider changing them.


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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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1201 W. Gregory Dr.
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e-mail: drnevich at uiuc.edu

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