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. 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/
