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
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]]
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
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]]
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