Hi, On Wed, Nov 24, 2010 at 4:17 PM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > Hi Henrik, > > Another question about the result is : is there a way to map the copy number > to the gene ID automatically?
You mean retrieving a list of genes contained in each DNAcopy segment ? No, this is not implemented in aroma.* You can use (for example) the biomaRt package to do this. > Also does aroma choose threshold for calling gain and loss? No, aroma.* just calls the DNAcopy::segment function for you, and this function just performs segmentation, and gives you the mean copy number in each segment. It does not call gains or losses. Cheers, Pierre > > Many thanks > > yan > > -----Original Message----- > From: aroma-affymetrix@googlegroups.com > [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson > Sent: 24 November 2010 15:08 > To: aroma-affymetrix > Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error > > Hi, > > great. Contrary to error messages, warnings are alright to get. > > /H > > On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >> Thank you Henrik, >> It works now, but I got some warning: >> >> process(ce, verbose=TRUE); >> Generating ChromosomeExplorer report... >> Loading required package: Cairo >> Generating ChromosomeExplorer report...done >> [1] TRUE >> Warning messages: >> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, >> logical.return = TRUE, : >> there is no package called 'Cairo' >> 2: In method(static, ...) : >> Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, >> /gs, C:\Program Files\Common Files/gs >> >> Are those warning messages serious? Could I ignore them? >> >> >> Yan >> >> -----Original Message----- >> From: aroma-affymetrix@googlegroups.com >> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson >> Sent: 23 November 2010 21:53 >> To: aroma-affymetrix >> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error >> >> Hi. >> >> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >>> Hi Henrik, >>> >>> Sorry, the error is after >>> cbs <- CbsModel(ds); >>> ce <- ChromosomeExplorer(cbs); >>> process(ce, verbose=TRUE); >> >> Ok, now the error message makes a bit more sense (it was my suspicion >> but I didn't want make guesses). >> >>> >>> >>> Generating ChromosomeExplorer report... >>> Loading required package: Cairo >>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable >>> to load shared library >>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll': >>> LoadLibrary failure: The specified module could not be found. >>> >>> And there is a pop out window saying: The program can't start because >>> libgsl-0.dll I smissing from your computer. Try reinstalling the program >>> to fix this program. >> >> I can reproduce this on 64-bit Windows 7 - you get the same error if >> you try library("GLAD"). It is because we utilize part of the GLAD >> package, if and only if it is *installed*, and otherwise we turn to >> backup solutions. What happens here is that *GLAD is installed but >> doesn't load*, which causes the error so that backup solutions doesn't >> kick in. In the next release I'll try to make sure the backup >> solutions will also work when there is an error load GLAD. In >> meanwhile, you can do this: >> >> WORKAROUND: >> >> 1. Uninstall the GLAD package (it doesn't work anyway): >> >>> remove.packages("GLAD") >> Removing package(s) from 'C:\Users\hb\R\win-library\2.12' >> (as 'lib' is unspecified) >> >>> library("GLAD") >> Error in library("GLAD") : there is no package called 'GLAD' >> >> That should do it. Let me know if it works for you. >> >> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL) >> is not installed on the system (hence the 'gsl' part of >> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in >> order to use the GLAD package, cf. >> http://bioconductor.org/packages/release/bioc/html/GLAD.html. There >> exist 32-bit binaries of GSL at >> http://gnuwin32.sourceforge.net/packages/gsl.htm. Unfortunately, it >> does not work for the 64-bit version of R on Windows 64-bit. It works >> if you do tricks an run the 32-bit version of R, but that is a rather >> inconvenient workaround. >> >> /Henrik >> >>> >>> >>> Yan >>> >>> -----Original Message----- >>> From: aroma-affymetrix@googlegroups.com >>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson >>> Sent: 23 November 2010 18:50 >>> To: aroma-affymetrix >>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error >>> >>> Hi. >>> >>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >>>> >>>> >>>> Dear all, >>>> >>>> I'm trying to do DNA segmentation, >>>> >>>> This is what I'm doing: >>>> >>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", >>> verbose=TRUE); >>>> >>>> ###this is done sucessfully >>>> >>>> # Segmentation >>>> >>>> cbs <- CbsModel(ds); >>>> >>>> >>>> >>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm >>> trying >>>> to use DNAcopy for segmentation. >>> >>> Is it really the case that you get that error when you do: >>> >>> cbs <- CbsModel(ds); >>> >>> or do you do anything else? Is suspect you do something more. >>> >>> Also, after you got the error, could you cut'n'paste the verbose >>> output including any error messages you get and send it to us? Also, >>> make sure to report what print(traceback()) gives immediate after >>> getting the error. >>> >>> /Henrik >>> >>> PS. The 'GLAD' package may indeed be used regardless of segmentation >>> method because it contains information about cytobands. >>> >>>> >>>> How to change it? >>>> >>>> >>>> >>>> Many thanks >>>> >>>> >>>> >>>> yan >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> ********************************************************************** >>>> >>>> This email and any files transmitted with it are confidential and >>>> >>>> intended solely for the use of the individual or entity to whom they >>>> >>>> are addressed. If you have received this email in error please notify >>>> >>>> the system manager (it.supp...@cancer.ucl.ac.uk). >>>> >>>> ********************************************************************** >>>> >>>> >>>> >>>> -- >>>> 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/ >>> >> >> -- >> 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/ > > -- > 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. 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