[BioC] is it possible to find sample batch # in CEL files?

[Wolfgang Huber]

Hi 

I haven't tried this in a while, but afaIcs the 'readAffy' function in the 'affy' package automatically populates the 'ScanDate' field in the resulting AffyBatch object, which you can access with syntax like
   protocolData(a)$ScanDate
where I have assumed that 'a' is an AffyBatch.

	Best wishes
	Wolfgang

Il giorno Jan 24, 2013, alle ore 2:43 PM, James F. Reid <reidjf at gmail.com> ha scritto:

> Hi Brian,
> 
> On 24/01/13 13:23, Brian Tsai wrote:
>> Hi,
>> 
>> I've been downloading raw CEL files from the gene expression omnibus, and
>> have been trying to process them -- i'd like to account for batch effect
>> when computing differential expression, but the authors didn't provide the
>> information explicitly in their annotations. Is this information
>> stored/retrievable through the CEL files through Bioconductor?
> you should be able to access the date the chip was scanned using the readCelHeader function provided in the affxparser package. Look for the 'datheader' entry.
> 
> James.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor