Hi, Yes this is correct.
Many thanks Ajanthah ________________________________________ From: aroma-affymetrix@googlegroups.com [aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson [...@stat.berkeley.edu] Sent: Sunday, July 18, 2010 11:28 AM To: aroma-affymetrix Subject: Re: [aroma.affymetrix] Analysis of GenomeWideSNP6.0 data Hi. On Fri, Jul 16, 2010 at 11:13 AM, Ajanthah Sangaralingam <a.sangaralin...@qmul.ac.uk> wrote: > 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. So, to make sure I don't misunderstand, you have an Affymetrix GenomeWideSNP_6 (GWS6) data set that contains tumors and for some, but not all of the you have matched normal samples, where "matched normal" mean a normal tissue or normal blood extract from the same patient as the tumor was taken. Is this correct? > 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. It is important to know which preprocessing method you are following. Since you are working with GWS6 arrays, I recommend that you use the CRMAv2 preprocessing method as described in vignette 'Estimation of total copy numbers using the CRMA v2 method (10K-GWS6)': http://aroma-project.org/vignettes/CRMAv2 Note the function doCRMAv2() which is convenient when you do not want to dig into the details. Since you are not mentioning probe-sequence normalization, it looks like you are indeed using CRMA v1. If so, I recommend that you use CRMA v2 instead. Using CRMA v2 will be really useful for you, as explained below. > 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. This is perfectly fine if you are using CRMA v2 (but not CRMA v1). As now clarified in the vignette, in addition to the CRMAv2 paper, you will get identical results with CRMAv2 regardless what other samples you put in your data set; the CRMAv2 method is truly a single-array method. It is only when you get to the step where calculate copy numbers relative to a pool of references you have to make a decision on what pool of reference samples you'll use. > 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. It actually can, as explained below. > > 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? The segmentation models, for instance CbsModel, segments each tumor either (a) to a matched normal, or (b) to a global reference. When you do (a), by definition there has to be an equal number of tumors as matched normals, whereas when you do (b), there can only be one reference sample specified. Example of paired tumor-normal segmentation: # A set of tumor samples dsT <- ... # A set of matched normal samples ordered such that they # match the ordering in the tumor data set 'dsT'. dsN <- ... sm <- CbsModel(dsT, dsN); Example of tumor-global reference segmentation: # A set of tumor samples dsT <- ... # A set of reference samples (can be normals or everything) dsR <- ... # Use the pool of all reference samples as the reference dfR <- getAverageFile(dsR); sm <- CbsModel(dsT, dfR); Note that 'dfR' is a single "virtual" array, not a data set. Did that above make sense? /Henrik > > 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/ > -- 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/ -- 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/
