Re: No CN estimates for SNP 6.0 (Was: Re: [aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays)
Hi, are you saying you do not get results from any chromosome? If so, that's a first very useful clue; if you get from some, something odd is going odd. Doing CN analysis on these chips is standard procedure, so it "should work" out of the box. In order to help you, what version are you using, i.e. output of sessionInfo(). Exactly what is script you are using? /Henrik > -Original Message- > From: Myriam Peyrard > Sent: den 16 juni 2009 17:01 > To: 'aroma-affymetrix' > Subject: RE: [aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays > > I have not gotten any answer about what can be wrong in my Aroma analysis > when I cannot visualize any CNVs or else on my chromsome maps in > ChromosomeExplorer. I tried now to run only one chromsome (nr 19) and again, > nothing on the plots even for 19. > I then looked at the Excel file in Cbs named "regions" and there are data in > there. So the analysis seems to work but not the visualization. > What shall I do/try? Is it a computer memory, capacity problem? > ChromosomeExplorer compatibility? > > Myriam On Thu, Jun 11, 2009 at 1:11 AM, Myriam Peyrard wrote: > > 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 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 pr
[aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays
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 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 -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays
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 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 -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays
Hi. On Thu, Jun 11, 2009 at 12:29 AM, Myriam 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 -~--~~~~--~~--~--~---
