Hi. On Thu, Jun 18, 2009 at 12:00 PM, han<[email protected]> wrote: > > Hi Henrik: > > Thanks for the help, I think that I found out why. I guess that > names of Nsp and Sty CEL files must be the same except the "Nsp/Sty" > part. Can "Nsp/Sty" appear any part in the file name?
This is documented in the vignette 'Total copy number analysis (10K, 100K, 500K)': http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis <quote> Samples that are hybridized to multiple chip types, are identified by their sample names, that is, sample tags are ignore. For instance, CEL files Mapping250K_Nsp/1-288,2006-10-03.cel and Mapping250K_Sty/1-288,2006-10-16.cel are identified to be of the same sample and their raw CNs are merged before fitting GLAD. </quote> To learn about names, tags, fullnames etc, see Page 'Names, tags, and filenames': http://groups.google.com/group/aroma-affymetrix/web/file--pathnames-2 (Make sure to read all those introductory pages. Suggestions for improvements are always welcomed.) Note, you do not have to rename you files to achieve this, but instead you can at any step of your analysis set a so called full names translator, which you can use to translate the fullname the way you want aroma.affymetrix to see them. Any output files will be based on the new translated fullnames (this latter property might be something we will change in the future). For an example how to use these, see Vignette 'Empirical probe-signal densities and rank-based quantile normalization': http://groups.google.com/group/aroma-affymetrix/web/empirical-probe-signal-densities-and-rank-based-quantile-normalization > > By the way, what are the two dotted lines below and above the zero > line. I guess that there are thresholds values, but what exactly are > they and how to get the values? They are just there for historical reasons and hard coded to correspond to *observed* log2(C/2) ratio levels [such that log2(C/2) = 0 for C=2] where C=1 and C=3, i.e. log2(1) = -1 and log2(3/2) = 0.58. /Henrik > > Thanks again. > > Han Chang > > On Jun 18, 12:16 pm, Henrik Bengtsson <[email protected]> wrote: >> See earlier CRMA (v1) vignette 'Total copy number analysis (10K, 100K, 500K)' >> >> http://groups.google.com/group/aroma-affymetrix/web/total-copy-number... >> >> on how these are combined in the segmentation step after being >> preprocessed separately. >> >> /Henrik >> >> On Thu, Jun 18, 2009 at 8:53 AM, han<[email protected]> wrote: >> >> > Dear Henrik: >> >> > I am processing 500k data for cell-lines, following your CRMA2 >> > example, then using CBS for seqgmentation "cbs <- CbsdModel >> > (cesNList)"; than used ChromosomeExplorer to dsiplay, and used >> > "getRegions" to get segment infomation. >> >> > My question is how can I get combined Nsp+Sty plots and segments? >> >> > Thanks; >> >> > Han Chang > > > --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
