Moreover, chrom 1 and 2, in all samples, seems not to have been done, (in grey shade when browsing acrross chromosomes and samples. Myriam
-----Original Message----- From: Myriam Peyrard [mailto:myriam.peyr...@ki.se] Sent: den 11 juni 2009 10:09 To: 'aroma-affymetrix@googlegroups.com' Subject: RE: [aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays Importance: High OK, nice to hear, about the warnings. Then I do: display(ce) and started to look in my different samples, all chromosomes. Seems that there is not a single CNV variation there? I did the normalization as non-paired sample sets, with average calculated with all samples: cbs <- CbsModel(cesN) Is this a normal output? I expected to have many variations and to have to sort them out in different ways. Now, I think something has gone wrong instead. Any ideas? Myriam -----Original Message----- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson Sent: den 11 juni 2009 09:38 To: aroma-affymetrix@googlegroups.com Subject: [aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays Hi. On Thu, Jun 11, 2009 at 12:29 AM, Myriam <myriam.peyr...@ki.se> wrote: > > Dear all, > > I have gone through a number of steps in the analysis of 28 arrays of > the Genomewide6.0 type and all seems OK until now: > > #Fitting copy-number model and displaying results > ####################################################################### > ce <- ChromosomeExplorer(cbs) > ce > > #ChromosomeExplorer: > #Name: CLP > #Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY > #Number of arrays: 28 > #Path: reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs > #RAM: 0.00MB > > process(ce, chromosomes=c > (1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23), > verbose=verbose) FYI, you can write the above much shorter: process(ce, chromosomes=1:23, verbose=verbose) > > And the end of the output after many hours run, looks like this: > #20090610 02:17:03| Writing CN regions...done > #20090610 02:17:03|Generating ChromosomeExplorer report...done > #[1] TRUE > #There were 50 or more warnings (use warnings() to see the first 50) > > I am looking at the 50 first warnings and I see that many are of the > same type. here comes an example of one of the each category of > warning. What shall I do now with each of those? You don't have to do anything. These warnings are alright and expected. No worries here. If you on the other hand get *errors* then you have to worry, but those will halt the script immediately. /Henrik > 1: In library(package, lib.loc = lib.loc, character.only = > TRUE, ... : > there is no package called 'Cairo' > 2: In method(static, ...) : > Ghostscript not found. Searched directories: C:/gs, C:\Program/gs, / > gs, C:\Program\Delade filer/gs > 3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... : > array has repeated maploc positions > > 4: In plotDev(pathname, width = width, height = height) : > Unable to allocate bitmap > 5: In plotDev(pathname, width = width, height = height) : opening > device failed > 6: In log(theta/thetaRef, base = 2) : NaNs produced > 7: In log(theta * thetaRef, base = 2) : NaNs produced > 8: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... : > array has repeated maploc positions > > Thanks a lot in adavnce for any help! > Myriam > > > > > > > > --~--~---------~--~----~------------~-------~--~----~ 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 aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
