[BioC] Error using arrayQuality and Agilent txt files

Valerie Obenchain vobencha at fhcrc.org
Sat Oct 16 03:05:57 CEST 2010

On 10/14/2010 02:30 AM, F. Javier López wrote:
>   Hi Valerie,
>   Thank you very much for your answer.
>   I have updated R and BioC and the problem still persists. 
Yes I get the errors too. There are several problems in the arrayQuality
package and the maintainers have not updated the package in some time. 
I have cc'd them on this message in case they are interested in
addressing them.
> I also had a
> look at the arrayQualityMetrics package, but I am quite interested in the
> quality-control measures calculated by agQuality that I cannot find in the
> arrayQualityMetrics.

I'm not sure which quality measures you are interested in. If
arrayQualityMetrics doesn't have what you need you may want to look at
the capabilities of the limma package. See the Linear Models for
Microarray Data User's Guide, Chapter 5 Quality Control.

The marray package would be another place to look.


>   Thank you!
>   Javier
> Hi Javier,
>> You are using an out of date version of R and Bioconductor. You should
>> update to R 2.11 / BioC 2.6 or wait until next week when R 2.12 / BioC
>> 2.7 will be available.
>> http://www.bioconductor.org/install/index.html
>> I would suggest using the arrayQualityMetrics package instead of
>> arrayQuality.  The arrayQuality package should have the functionality
>> you are looking for along with helpful documentation and active
>> maintainers.
>> Let me know if you have problems.
>> Valerie
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