[BioC] Exception thrown in ReadAffy() when reading Hu-133B files in a GEO Dataset

[Sean Davis]

On Mon, Sep 9, 2013 at 3:52 PM, Peterson, Leif
<LEPeterson at houstonmethodist.org> wrote:
> When using the straightforward "ReadAffy()" syntax to read Affy arrays, I am experiencing an exception which is being thrown when the reader hits HU133B file in a particular GEO dataset.   Is there an optimal way to read Hu-133A arrays separately from HU-133B arrays (.CEL files) from an untarred GEO data set?
>

Hi, Leif.

You'll need to either:

1) Put arrays from each platform in separate directory
or
2) Supply a vector of filenames for each array platform to ReadAffy

You can use the GEOquery or GEOmetadb packages to associate the arrays
to the correct platform.

Sean