[BioC] R: Problem in reading JPEG files for CGH arrays

[Robert Gentleman]

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: 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 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