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

[Ben Bolstad]

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
> 
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Ben Bolstad <bmb at bmbolstad.com>
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