Hi, I have been doing some paired total copy number analysis in aroma afyymetrix. The dataset I have is complicated for haf the dataset I have reference samples, for the other half I will do an unpiared analysis. I alos have data from many different tomor types not just one - I do not have the sample number of samples from each type of tumor.
My questions are: When doing a paired analysis - the normal and tumour data have there own directories and allelic cross talk calibration, summarization and PCR fragment length normlization is all done separately. Is this tue for the different tumor types as well - should they be treated separately for all of tehse stages or can all the tumor types be put into one tumour directory. Also, I am unable to extarct the reference samples that I want after normaization to compare to the matching sanmples say in another tumor type. Segmentation models cannot be fit unless the number of samples match exactly. Does this mean that I need to do all the stages again for the subsets of reference samples that have matching pairs in the other tumor types? Many thanks Ajanthah This email may contain information that is privileged, confidential or otherwise protected from disclosure. It must not be used by, or its contents copied or disclosed to, persons other than the addressee. If you have received this email in error please notify the sender immediately and delete the email. This message has been scanned for viruses. -- 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/
