[BioC] Using read.maimages() with Imagene output files.

Gordon Smyth smyth at wehi.edu.au
Thu Aug 14 13:24:12 MEST 2003

Hi Nick,

You're closer to me, both geographically and time-zone wise, than Luke is 
so could you please send me four imagene files, i.e., both channels for two 
different arrays. Please zip or otherwise compress the files and then email 
them to me in four separate emails.

Also, does your scanner produce a separate gene allocation list specifying 
which gene corresponds to which spot? At the moment, limma provides direct 
support only for Genepix allocation lists.


At 11:35 AM 14/08/2003, Nick Matigian wrote:
>Hi  Gordon
>I have the same problem as Luke. So if he does not send you any ImaGene 
>files I can.
>Nick Matigian
>Queensland Centre for Schizophrenia Research
>Queensland Institute of Medical Research
>nickMa at qimr.edu.au
>Telephone: 61 7 3362 0308
>Facsimile: 61 7 3845 3508
>Queensland Institute of Medical Research
>Post Office Box Royal Brisbane Hospital
>Herston, Queensland, Australia, 4006
>-----Original Message-----
>From:   Gordon Smyth [SMTP:smyth at wehi.edu.au]
>Sent:   Thursday, August 14, 2003 10:25 AM
>To:     Luke Whitaker
>Cc:     bioconductor at stat.math.ethz.ch
>Subject:        Re: [BioC] Using read.maimages() with Imagene output files.
>Dear Luke,
>At 01:31 AM 14/08/2003, Luke Whitaker wrote:
> >I am attempting to analyse some microarray data that has been
> >scanned using a program called Imagene and I would like to try and
> >use limma for the analysis. I was wondering if it might be possible
> >to use read.maimages() to read these data into R.
> >
> >It appears to me that read.maimages() expects both the red and green
> >signals to be present in a single file. Imagene produces separate files for
> >the red and green signals. Does anyone out there have any suggestions how
> >to proceed ?
>What you say is correct - read.maimages does not support Imagene files, nor
>does any other function in Bioconductor.
>If you would be prepared to make available to me some examples of imagene
>data files, then I will add imagene functionality to read.maimages.
> >Thanks in advance,
> >
> >Luke Whitaker
> >Inpharmatica
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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