Dear Group, I have 28 samples of tumour normal pairs, run on 2 GenomeWideSNP6.0 arrays several months apart. Some of the pairs have members on different chips (ie tumor on one, normal on the other). I am not sure about the best way to normalise the data such that these split pairs can be used for downstream analysis. The plan is for ASCRMA, TumorBoost and then PSCBS.
I have applied ASCRMA to each array separately. Probe density plots pre and post this normalisation are attached. It seems that there is still some room for improvement. Thank you and all the best for the new year. Regards, Peter -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
