Dear Aroma Community, I want to create segmentation file for the CCLE dataset and want to use HapMap as the normal samples. However, I don't know how to find the most similar normal samples that correspond to each of my tumor samples. As I understand it, I have to make pairwise comparison between normal and tumor. In the CCLE website they describe it as "Copy numbers were then inferred based upon estimating probe set specific linear calibration curves, followed by normalization by the most similar HapMap normal samples."
The reason I want to be able to re-create CCLE's segmentation file is because I want to apply the same pipeline they used to another dataset to create segmentation file. I am trying to use "aroma.affymetrix," but not sure how to use the HapMap samples with the CCLE samples. Also, none of the GenomeWideSNP_6 Release from 22-30 match exactly with the CCLE segmentation file that is provided in their website. CCLE: http://www.broadinstitute.org/ccle/data/browseData;jsessionid=B67BBEEE6DE091440D4F28F7332C2C5D?conversationPropagation=begin Thank you, Naif -- 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
