it's hard to say what causing this, but if you see it in several
samples at the same location, then my immediate thought is that you
reference signal may carry it.  Are you using the average of the pool
of all samples as a reference or how do you calculate it?   How many
samples to you have in your reference pool?  CN polymorphic regions
that are frequent enough in your population could cause this, but then
it should be a real biological signal, which you say it isn't.

Are you using the full or the default GenomeWideSNP_6 CDF?  Affymetrix
removed several CN loci from the former to make the latter - CN loci
that they found to be poor for CN analysis.  This could also be a
reason though those loci should be scattered fairly randomly along the

You could also check if there is a difference between the signals from
SNPs and CN loci.  If there is, that would indicate that there is some
artifacts on the arrays.

Also, are you really sure you are using the correct annotation data?
For instance, if you use the full CDF to generate the data, but only
the default for extracting genome locations (assuming the same
ordering of row indices), such weird things may show up.  If you plot
your data using the ChromosomeExplorer, this should be taken care of

Also, do some QC plots using ArrayExplorer; there might be spatial
artifacts, although it sounds unlikely.

Sorry, not much help, but at least some directions for


On Jul 21, 5:34 pm, Matt Wilkerson <mdwilk...@gmail.com> wrote:
> Hello,
> I have detected what I think is an array quality issue and wanted to get
> others' opinions about this phenomena.
> I observed this issue on chromosome views of CN from SNP6 arrays.  It looks
> like a "smearing" effect where CN has irregular values and a range of large
> negative numbers to zero within specific regions.  The regions at which this
> happens are identical in affected samples and occur on basically all
> chromosomes.  This smearing is not cancer DNA segment loss, where probes
> belonging to a segment have similar CN values.  In a group of about 70
> arrays, 1/3 of the arrays have this issue and the others have expected
> segments of discrete amplifications/deletions.  I have compared specimen,
> technical, and array characteristics to try to find a batch or quality
> issues, but the effect appears so far to be randomly occuring.
> I put an example 
> at:http://www.unc.edu/~mwilkers/artifact.png<http://www.unc.edu/%7Emwilkers/artifact.png>
> In the plot, the points are probes. Axes are base position and log2 median
> centered copy number.  The lines are segments overlaid.  The colors are not
> important.
> I don't think this is an aroma issue - I detect the phenomena using
> apt-copynumber-workflow also.  The only affymetrix summary option that
> associated with the artifact samples was "allele summarization mean".  The
> artifact arrays had lower values.
> Also, I have used aroma successfully with 250K_Sty arrays often and never
> seen this phenomena.
> My question:
> Has anyone seen this phenomena before?
> Does anyone have an explanation or suggestion?
> Thank you,
> Matt Wilkerson
> Lineberger Comprehensive Cancer Center
> University of North Carolina at Chapel Hill

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

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