  Hi Valerie,

  Thank you very much again. I will have a look at the limma and marray
packages.

  I forgot to say I also tried using an marrayRaw object but the result was:

> mraw <-
read.Agilent(c("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt",
"US85003608_251486821883_S01_GE2-v5_10_Apr08_1_2.txt",
"US85003608_251486821883_S01_GE2-v5_10_Apr08_1_3.txt",
"US85003608_251486821883_S01_GE2-v5_10_Apr08_1_4.txt"))
Reading ...  ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt
Reading ...  ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_2.txt
Reading ...  ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_3.txt
Reading ...  ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_4.txt

> maQualityPlots(mraw)
[1] TRUE
[1] TRUE
[1] TRUE
Error in .subset2(x, i, exact = exact) :
   attempt to select less than one element


  Best Wishes,

  Javier




On 10/14/2010 02:30 AM, F. Javier L?pez 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.
http://bioconductor.org/help/bioc-views/2.7/bioc/html/limma.html

The marray package would be another place to look.

Valerie

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