MBNI CDF
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alex lam RI ▴ 310
@alex-lam-ri-1491
Last seen 7.7 years ago
Dear BioC users, I am going to use the custom CDF released by MBNI for the array rae230a. Does anyone know of any methods / webpage for getting basic statistics such as how many probesets did not match ensembl, how many probes were removed because of SNPs ... etc? Many thanks, Alex -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute
cdf cdf • 599 views
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Yuan Jian ▴ 250
@yuan-jian-2603
Last seen 6.3 years ago
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Hi Yuan, Please don't hijack existing threads and just overwrite the subject. If you want to ask a new question, send a new email. Yuan Jian wrote: > Hello, > > I have installed EBImage in windows XP: > > source("http://www.braju.com/R/hbLite.R") > > biocLite("EBImage") > > but when I do > >library(EBImage) > the following error message box appeared: > "This application has failed to start because libgdk- win32-2.0-0.dll was not found, > Re-installing the application may fix this problem." > > I re-installed, the problem still is there. > can you help me to solve the problem? Yes. The error message isn't talking about EBImage, it is talking about the other required functions that you need to install. See here for the required Windows dependencies. http://www.ebi.ac.uk/~osklyar/EBImage/ Best, Jim > > > > > > > > > "alex lam (RI)" <alex.lam at="" bbsrc.ac.uk=""> wrote: > Dear BioC users, > > I am going to use the custom CDF released by MBNI for the array rae230a. > Does anyone know of any methods / webpage for getting basic statistics > such as how many probesets did not match ensembl, how many probes were > removed because of SNPs ... etc? > > Many thanks, > Alex > -------------------------------------------- > Alex C. Lam > Roslin Institute (Edinburgh) > Midlothian > EH25 9PS > United Kingdom > Tel: +44 131 5274471 > > Roslin Institute is a company limited by guarantee, registered in > Scotland (registered number SC157100) and a Scottish Charity (registered > number SC023592). Our registered office is at Roslin, Midlothian, EH25 > 9PS. VAT registration number 847380013. > > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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Dear Jian, This is not EBImage error, but GTK configuration error, which is independent on the package: the package fails to find one of the most basic GTK libraries that are required for its proper functioning. The package requires at least 2 dependencies that must be installed separately on Windows. biocLite does not do that because those are not R, but system dependencies. GTK containing GDK is one of those. Unfortunately, often people use biocLite without thinking that many packages require system-level dependencies, which are not installed and biocLite does not warn about it. Have you checked the installation manual for the package? Please check this manual, ensure that everything what is in there is done. If it still does not work check if {GTK}\lib is in your PATH along with {GTK}\bin. If this all does not help, please post more details: versions of R, EBImage, GTK, ImageMagick that you are trying to use; the contents of your PATH variable in part concerning GTK and ImageMagick Best, Oleg Yuan Jian wrote: > Hello, > > I have installed EBImage in windows XP: > > source("http://www.braju.com/R/hbLite.R") > > biocLite("EBImage") > > but when I do > >library(EBImage) > the following error message box appeared: > "This application has failed to start because libgdk- win32-2.0-0.dll was not found, > Re-installing the application may fix this problem." > > I re-installed, the problem still is there. > can you help me to solve the problem? > > > > > > > > > "alex lam (RI)" <alex.lam at="" bbsrc.ac.uk=""> wrote: > Dear BioC users, > > I am going to use the custom CDF released by MBNI for the array rae230a. > Does anyone know of any methods / webpage for getting basic statistics > such as how many probesets did not match ensembl, how many probes were > removed because of SNPs ... etc? > > Many thanks, > Alex > -------------------------------------------- > Alex C. Lam > Roslin Institute (Edinburgh) > Midlothian > EH25 9PS > United Kingdom > Tel: +44 131 5274471 > > Roslin Institute is a company limited by guarantee, registered in > Scotland (registered number SC157100) and a Scottish Charity (registered > number SC023592). Our registered office is at Roslin, Midlothian, EH25 > 9PS. VAT registration number 847380013. > > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, England * +44-1223-494466
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@james-w-macdonald-5106
Last seen 14 hours ago
United States
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf readme.htm alex lam (RI) wrote: > Dear BioC users, > > I am going to use the custom CDF released by MBNI for the array rae230a. > Does anyone know of any methods / webpage for getting basic statistics > such as how many probesets did not match ensembl, how many probes were > removed because of SNPs ... etc? > > Many thanks, > Alex > -------------------------------------------- > Alex C. Lam > Roslin Institute (Edinburgh) > Midlothian > EH25 9PS > United Kingdom > Tel: +44 131 5274471 > > Roslin Institute is a company limited by guarantee, registered in > Scotland (registered number SC157100) and a Scottish Charity (registered > number SC023592). Our registered office is at Roslin, Midlothian, EH25 > 9PS. VAT registration number 847380013. > > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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