[BioC] Non windows utility for CEL file Binary to Ascii format conversion

[Robert Gentleman]

And I can only underscore Ben's point:
if you are writing a package, please try to use some of the standard 
tools to read/write files, compute simple summary statistics and use 
standard data structures. While it may take a little longer initially 
your code will work better with Bioconductor and you will get most new 
features more easily than writing them yourself. And of course these 
other packages have often been widely tested, relieving you of such a 
need.  As always, folks here in Seattle are available to help with such 
integration.

  best wishes
    Robert


Ben Bolstad wrote:
> Although this doesn't really directly answer your question ....
> 
> You might consider prompting the authors of the sscore package to
> consider building on top of the standard structures and parsers. Based
> upon the vignette for this package it appears that they already
> partially do so by making use of ReadAffy() to build an AffyBatch. From
> what I can tell sscore wants the original CEL files to get the
> "[OUTLIERS]" section.
> 
> They could get the "outliers" section from a specified CEL file like
> this (using the parsers in affyio 1.1.7 or later which is what
> ReadAffy() is using).
> 
> myCEL <- read.celfile("/path/to/mycelfilename.CEL")
> myCEL$OUTLIERS
> 
> I'm sure there is also a perfectly acceptable way to do it using the
> affxparser package.
> 
> 
> Users shouldn't really be forced to have to make manual file format
> conversions. Instead the parsers should handle this all automatically.
> 
> Best,
> 
> Ben
> 
> 
> 
> On Fri, 2006-08-11 at 22:02 -0400, Lakshmanan Iyer wrote:
>> Hi
>> The SScore package reads ascii  format affymatrix CEL files only and I have
>> a few binary format CEL files.
>> Affymatrix provides a tool that can be used to convert the formats but this
>> is for windows only!
>>
>> I am wondering if there is any other utiltiy that allows one to convert the
>> binary format Affymatrix CEL files to Ascii format.
>> -Thanks
>> -Lax
>> Tufts University School of Medicine
>> Tufts-New England College of Medicine
>> Boston
>> MA
>>
>> 	[[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