Hi all, I'm trying to normalize several thousands of tumor samples using aroma. The BAF profiles I get using
> AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=FALSE) are quite noisy, so I have started using ACNE for getting 'cleaner' ones. The problem is that I don't want to use the tumors as a reference, because some of them have a lot of alterations. With aroma I used the 'target=0' option to get log intensities and then I normalized them against my pool of normals or against them matched normal if available just subtracting the values. For ACNE it seems I have to specify the reference, so I created folders for each of my matched pairs and used > NmfSnpPlm(csN, mergeStrands=TRUE, refs=c(FALSE, TRUE)) To indicate that the second array is the normal and the first the tumor. Is this the best way to proceed in my situation? The former command produces the following values for chromosome 2: > summary(data) total freqB Min. : 0.0 Min. : NA 1st Qu.: 0.0 1st Qu.: NA Median : 905.6 Median : NA Mean : 2345.2 Mean : NaN 3rd Qu.: 4192.8 3rd Qu.: NA Max. :53200.6 Max. : NA NA's :153732 So it's clear that I'm doing something wrong. Does anyone know what is it? Thanks in advance, Oscar Oscar M. Rueda, PhD Postdoc, Breast Cancer Functional Genomics Cancer Research UK Cambridge Research Institute Li Ka Shing Centre Robinson Way Cambridge CB2 0RE England This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. -- 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/