Blobs

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Yogi Sundaravadanam ▴ 320

@yogi-sundaravadanam-2312

Last seen 9.6 years ago

Hi all, I was looking at some exon arrays and a lot of the CEL file images have blobs/smears I was wonder if we have to repeat the experiment or if there were tools in bioconductor that could possibly correct these kind of errors. Thanking you in advance Cheers Yogi [[alternative HTML version deleted]]

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ADD COMMENT • link updated 15.8 years ago by Steve Lianoglou ★ 13k • written 15.8 years ago by Yogi Sundaravadanam ▴ 320

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 14 months ago

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Hi, On Jul 9, 2008, at 1:02 AM, Yogi Sundaravadanam wrote: > Hi all, > > I was looking at some exon arrays and a lot of the CEL file images > have > blobs/smears > I was wonder if we have to repeat the experiment or if > there were tools in bioconductor that could possibly correct these > kind > of errors. Check out the harshlight package. I've been meaning to look into it more myself, but I believe it tries to deal with the issues you mention. R Package: http://bioconductor.org/packages/2.2/bioc/html/Harshlight.html Publication: http://www.biomedcentral.com/1471-2105/6/294 Hope that helps. -steve

ADD COMMENT • link 15.8 years ago Steve Lianoglou ★ 13k

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There's also MblobR. reference: Song, J. S.; Maghsoudi, K.; Li, W.; Fox, E.; Quackenbush, J. & Liu, X. S. Microarray blob-defect removal improves array analysis. Bioinformatics, 2007, 23, 966-971 cheers, Mark On 10/07/2008, at 12:26 AM, Steve Lianoglou wrote: > Hi, > > On Jul 9, 2008, at 1:02 AM, Yogi Sundaravadanam wrote: > >> Hi all, >> >> I was looking at some exon arrays and a lot of the CEL file images >> have >> blobs/smears >> I was wonder if we have to repeat the experiment or if >> there were tools in bioconductor that could possibly correct these >> kind >> of errors. > > Check out the harshlight package. I've been meaning to look into it > more myself, but I believe it tries to deal with the issues you > mention. > > R Package: > http://bioconductor.org/packages/2.2/bioc/html/Harshlight.html > > Publication: > http://www.biomedcentral.com/1471-2105/6/294 > > Hope that helps. > > -steve > > _______________________________________________ > 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

ADD REPLY • link 15.8 years ago Mark Cowley ▴ 400

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Hi Mark, On Jul 13, 2008, at 6:58 PM, Mark Cowley wrote: > There's also MblobR. > reference: > Song, J. S.; Maghsoudi, K.; Li, W.; Fox, E.; Quackenbush, J. & Liu, > X. S. > Microarray blob-defect removal improves array analysis. > Bioinformatics, 2007, 23, 966-971 I just downloaded this to check it out ... have you been using it all? After downloading all the dependency jars[1], I realized that it only opens CEL files saved as version 4 (the binary one), while the files I have are version 3[2]. Do you (or anybody else) know if there is an easy way to convert between versions of CEL files? Thanks, -steve [1] For anybody else who's trying to run this, you'll need to have in your classpath: * junit.jar: http://junit.org/ * swing-layout.jar: https://swing-layout.dev.java.net/ [2] Affy cel version info: http://www.stat.lsa.umich.edu/~kshedden/Cou rses/Stat545/Notes/AffxFileFormats/cel.html -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Cornell Medical College http://cbio.mskcc.org/~lianos

ADD REPLY • link 15.8 years ago Steve Lianoglou ★ 13k

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Use affxparser Kasper On Jul 14, 2008, at 7:42 AM, Steve Lianoglou wrote: > Hi Mark, > > On Jul 13, 2008, at 6:58 PM, Mark Cowley wrote: > >> There's also MblobR. >> reference: >> Song, J. S.; Maghsoudi, K.; Li, W.; Fox, E.; Quackenbush, J. & Liu, >> X. S. >> Microarray blob-defect removal improves array analysis. >> Bioinformatics, 2007, 23, 966-971 > > I just downloaded this to check it out ... have you been using it > all? After downloading all the dependency jars[1], I realized that > it only opens CEL files saved as version 4 (the binary one), while > the files I have are version 3[2]. > > Do you (or anybody else) know if there is an easy way to convert > between versions of CEL files? > > Thanks, > -steve > > [1] For anybody else who's trying to run this, you'll need to have > in your classpath: > * junit.jar: http://junit.org/ > * swing-layout.jar: https://swing-layout.dev.java.net/ > > [2] Affy cel version info: http://www.stat.lsa.umich.edu/~kshedden/C ourses/Stat545/Notes/AffxFileFormats/cel.html > > -- > Steve Lianoglou > Graduate Student: Physiology, Biophysics and Systems Biology > Weill Cornell Medical College > > http://cbio.mskcc.org/~lianos > > _______________________________________________ > 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

ADD REPLY • link 15.8 years ago Kasper Daniel Hansen ★ 6.5k

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Hi Steve and Kasper, Using affxparser would keep things in R/Bioconductor, but there is also apt-cel-convert from the Affymetrix Power Tools http://www.affymetrix.com/support/developer/powertools/changelog/index .html cheers, Mark On 15/07/2008, at 4:00 AM, Kasper Daniel Hansen wrote: > Use affxparser > > Kasper > > On Jul 14, 2008, at 7:42 AM, Steve Lianoglou wrote: > >> Hi Mark, >> >> On Jul 13, 2008, at 6:58 PM, Mark Cowley wrote: >> >>> There's also MblobR. >>> reference: >>> Song, J. S.; Maghsoudi, K.; Li, W.; Fox, E.; Quackenbush, J. & >>> Liu, X. S. >>> Microarray blob-defect removal improves array analysis. >>> Bioinformatics, 2007, 23, 966-971 >> >> I just downloaded this to check it out ... have you been using it >> all? After downloading all the dependency jars[1], I realized that >> it only opens CEL files saved as version 4 (the binary one), while >> the files I have are version 3[2]. >> >> Do you (or anybody else) know if there is an easy way to convert >> between versions of CEL files? >> >> Thanks, >> -steve >> >> [1] For anybody else who's trying to run this, you'll need to have >> in your classpath: >> * junit.jar: http://junit.org/ >> * swing-layout.jar: https://swing-layout.dev.java.net/ >> >> [2] Affy cel version info: http://www.stat.lsa.umich.edu/~kshedden/ Courses/Stat545/Notes/AffxFileFormats/cel.html >> >> -- >> Steve Lianoglou >> Graduate Student: Physiology, Biophysics and Systems Biology >> Weill Cornell Medical College >> >> http://cbio.mskcc.org/~lianos >> >> _______________________________________________ >> 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 >

ADD REPLY • link 15.8 years ago Mark Cowley ▴ 400

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