[BioC] looking for data file for ATH1 (GPL198)

Loraine, Ann Ann.Loraine at uncc.edu
Sat Oct 5 06:01:35 CEST 2013

Thank you for getting back to me so quickly.

I will try to make an frma data file for the ATH1/GPL198 array using

Follow-up question:

Can you explain what is meant by this line in the frmaTools vignette?

"Create batch ids based on your arrays."

and then:

 vectors <- makeVectorsAffyBatch(files, batch.id)

The help documentation says "batch.id" is a vector.

I understand that I need to associate CEL file names with batches, but I
don't understand how the structure of "batch.id" allows me to do this.

What should "batch.id" contain and how do I relate it to "files" ?

On 10/4/13 5:11 PM, "Matthew McCall" <mccallm at gmail.com> wrote:

>Unfortunately there isn't currently an fRMA implementation for ATH1.
>It is on the to-do list, but as you might imagine, that list is very
>long. You could create your own implementation using the frmaTools
>package described in:
>McCall MN* and Irizarry RA (2011). Thawing Frozen Robust Multi-array
>Analysis (fRMA), BMC Bioinformatics, 12:369.
>On Fri, Oct 4, 2013 at 12:32 PM, Loraine, Ann <Ann.Loraine at uncc.edu>
>> Hello,
>> I would like to use fRMA to process data from the ATH1 (GPL198)
>> from Affymetrix.
>> Is there a data file I can use for that array ­ e.g., something like
>> hgu133afrmavecs but for the GPL198/ATH1 platform?
>> If yes, what is it called and how do I load it?
>> Thank you and best wishes,
>> Ann Loraine
>> -------------------------------
>> Ann Loraine, Ph.D.
>> Associate Professor
>> Department of Bioinformatics and Genomics
>> University of North Carolina at Charlotte
>> North Carolina Research Campus
>> 600 Laureate Way
>> Kannapolis, NC 28081
>> 704-250-5750
>> aloraine at uncc.edu
>> http://www.transvar.org
>> http://www.bioviz.org
>> http://www.uncc.edu
>Matthew N McCall, PhD
>112 Arvine Heights
>Rochester, NY 14611
>Cell: 202-222-5880

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