Hi Henrik, Another question about the result is : is there a way to map the copy number to the gene ID automatically? Also does aroma choose threshold for calling gain and loss?
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/
