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