Problem in reading JPEG files for CGH arrays
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@alberto-goldoni-711
Last seen 10.2 years ago
Dear all is it possible to read jpeg files from a Agilent scanner regarding CGH arrays with R....i don't know if pakages like aCGH or GLAD are able to import and translate in a txt file this kind of image. ----------------------------------------------------- Dr Alberto Goldoni, PhD IT Lan Manager Medical Genetics Unit S. Orsola-Malpighi Hospital Via Massarenti n.9, Pad 11 40100 Bologna, Italy Mobile Phone: 338-4145970 Fax: 051-636-4004 alberto.goldoni at eurogene.org www.eurogene.org www.lagem.it
aCGH Genetics aCGH GLAD aCGH Genetics aCGH GLAD • 1.5k views
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@sean-davis-490
Last seen 3 months ago
United States
On Thu, Jan 22, 2009 at 9:37 AM, Alberto Goldoni < alberto.goldoni@eurogene.org> wrote: > Dear all > is it possible to read jpeg files from a Agilent scanner regarding CGH > arrays with R....i don't know if pakages like aCGH or GLAD are able to > import and translate in a txt file this kind of image. > I think that there is no software available in Bioconductor to do image analysis of orange-packed arrays. (Someone will chime in if I am incorrect here, I am sure.) Also, the JPEG images are likely not to be of use, anyway. You would need the tiff images to do the image analysis. Your best bet is to go back to the original producers of the data and ask them for the text files. Sean [[alternative HTML version deleted]]
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So if i have understood there is no program inside or external to R that can convert a jpeg or tiff file in a txt. so if i have agilent tiff file i need agilent program in order to obtain a txt final file and then of course i can use glad or acgh etc best regards ----------------------------------------------------- Dr Alberto Goldoni, PhD IT Lan Manager Medical Genetics Unit S. Orsola-Malpighi Hospital Via Massarenti n.9, Pad 11 40100 Bologna, Italy Mobile Phone: 338-4145970 Fax: 051-636-4004 alberto.goldoni at eurogene.org www.eurogene.org www.lagem.it ________________________________________ Da: seandavi at gmail.com [seandavi at gmail.com] per conto di Sean Davis [sdavis2 at mail.nih.gov] Inviato: gioved? 22 gennaio 2009 16.54 A: Alberto Goldoni Cc: Bioconductor mailing list Oggetto: Re: [BioC] Problem in reading JPEG files for CGH arrays On Thu, Jan 22, 2009 at 9:37 AM, Alberto Goldoni <alberto.goldoni at="" eurogene.org<mailto:alberto.goldoni="" at="" eurogene.org="">> wrote: Dear all is it possible to read jpeg files from a Agilent scanner regarding CGH arrays with R....i don't know if pakages like aCGH or GLAD are able to import and translate in a txt file this kind of image. I think that there is no software available in Bioconductor to do image analysis of orange-packed arrays. (Someone will chime in if I am incorrect here, I am sure.) Also, the JPEG images are likely not to be of use, anyway. You would need the tiff images to do the image analysis. Your best bet is to go back to the original producers of the data and ask them for the text files. Sean
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On Thu, Jan 22, 2009 at 11:23 AM, Alberto Goldoni < alberto.goldoni@eurogene.org> wrote: > So if i have understood there is no program inside or external to R that > can convert a jpeg or tiff file in a txt. > Assuming you are talking about freely available software, I do not think so. That said, I haven't looked into image analysis software in a couple of years, so I would be happy to hear otherwise. > > so if i have agilent tiff file i need agilent program in order to obtain a > txt final file and then of course i can use glad or acgh etc > Or another image analysis software that can deal with Agilent tiff images, assuming the arrays were scanned on an Agilent scanner; their tiff format uses some unusual tags and is composed of two layers. Sean > > best regards > ----------------------------------------------------- > Dr Alberto Goldoni, PhD > IT Lan Manager > Medical Genetics Unit > S. Orsola-Malpighi Hospital > Via Massarenti n.9, Pad 11 > 40100 Bologna, Italy > Mobile Phone: 338-4145970 > Fax: 051-636-4004 > alberto.goldoni@eurogene.org > www.eurogene.org > www.lagem.it > ________________________________________ > Da: seandavi@gmail.com [seandavi@gmail.com] per conto di Sean Davis [ > sdavis2@mail.nih.gov] > Inviato: giovedì 22 gennaio 2009 16.54 > A: Alberto Goldoni > Cc: Bioconductor mailing list > Oggetto: Re: [BioC] Problem in reading JPEG files for CGH arrays > > On Thu, Jan 22, 2009 at 9:37 AM, Alberto Goldoni < > alberto.goldoni@eurogene.org<mailto:alberto.goldoni@eurogene.org>> wrote: > Dear all > is it possible to read jpeg files from a Agilent scanner regarding CGH > arrays with R....i don't know if pakages like aCGH or GLAD are able to > import and translate in a txt file this kind of image. > > I think that there is no software available in Bioconductor to do image > analysis of orange-packed arrays. (Someone will chime in if I am incorrect > here, I am sure.) Also, the JPEG images are likely not to be of use, > anyway. You would need the tiff images to do the image analysis. Your best > bet is to go back to the original producers of the data and ask them for the > text files. > > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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]]
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On Thu, Jan 22, 2009 at 8:38 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Thu, Jan 22, 2009 at 11:23 AM, Alberto Goldoni < > alberto.goldoni at eurogene.org> wrote: > >> So if i have understood there is no program inside or external to R that >> can convert a jpeg or tiff file in a txt. >> > > Assuming you are talking about freely available software, I do not think > so. That said, I haven't looked into image analysis software in a couple of > years, so I would be happy to hear otherwise. > OK- I believe that EBImage will do what is wanted, it is an interface to ImageMagick. I suspect that you will need to write a fair amount of software to do any analysis of real interest, but the building blocks should be there. best wishes Robert > >> >> so if i have agilent tiff file i need agilent program in order to obtain a >> txt final file and then of course i can use glad or acgh etc >> > > Or another image analysis software that can deal with Agilent tiff images, > assuming the arrays were scanned on an Agilent scanner; their tiff format > uses some unusual tags and is composed of two layers. > > Sean > > >> >> best regards >> ----------------------------------------------------- >> Dr Alberto Goldoni, PhD >> IT Lan Manager >> Medical Genetics Unit >> S. Orsola-Malpighi Hospital >> Via Massarenti n.9, Pad 11 >> 40100 Bologna, Italy >> Mobile Phone: 338-4145970 >> Fax: 051-636-4004 >> alberto.goldoni at eurogene.org >> www.eurogene.org >> www.lagem.it >> ________________________________________ >> Da: seandavi at gmail.com [seandavi at gmail.com] per conto di Sean Davis [ >> sdavis2 at mail.nih.gov] >> Inviato: gioved?? 22 gennaio 2009 16.54 >> A: Alberto Goldoni >> Cc: Bioconductor mailing list >> Oggetto: Re: [BioC] Problem in reading JPEG files for CGH arrays >> >> On Thu, Jan 22, 2009 at 9:37 AM, Alberto Goldoni < >> alberto.goldoni at eurogene.org<mailto:alberto.goldoni at="" eurogene.org="">> wrote: >> Dear all >> is it possible to read jpeg files from a Agilent scanner regarding CGH >> arrays with R....i don't know if pakages like aCGH or GLAD are able to >> import and translate in a txt file this kind of image. >> >> I think that there is no software available in Bioconductor to do image >> analysis of orange-packed arrays. (Someone will chime in if I am incorrect >> here, I am sure.) Also, the JPEG images are likely not to be of use, >> anyway. You would need the tiff images to do the image analysis. Your best >> bet is to go back to the original producers of the data and ask them for the >> text files. >> >> Sean >> >> _______________________________________________ >> 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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