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:
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

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.

You received this message because you are subscribed to the Google Groups 
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

Reply via email to