[BioC] quality assessment of microarray using arrayQualityMetrics

[Amit]

Dear Wolfgang,

Thank you for your reply. I asked that question because
arrayQualityMetrics gives following error with MAList object:
#loading required libraries
>library(convert)
>library(arrayQualityMetrics)
#loading MAList object into R
> load("rat_norm_MA.RData")
> dim(rat_norm_MA$M)
[1] 20500   363
> dim(rat_norm_MA$A)
[1] 20500   363
> qm=arrayQualityMetrics(rat_norm_MA,"qm_rat")
Error in validObject(.Object) :
  invalid class "ExpressionSet" object: sampleNames differ between
assayData and phenoData
Error in arrayQualityMetrics(rat_norm_MA, "qm_rat") :
  The expressionset is a MAList and cannot be converted automatically
in a ExpressionSet. Try to convert it manually.

Hence, I wish to know if arrayQualityMetrics works on M or A, so that
I could convert one of these to ExpressionSet and run
arrayQualityMetrics on it.

Best!
Amit

On Thu, Apr 15, 2010 at 12:02 AM, Wolfgang Huber <whuber at embl.de> wrote:
> Dear Amit
>
> have a look at the manual page of the 'arrayQualityMetrics' function. There,
> you can see that it accepts 'MAList' objects directly, and extracts the
> needed information from that.
>
> Another way to learn more about this package is its vignette, which you can
> view with
>  vignette("arrayQualityMetrics")
>
>        Best wishes
>        Wolfgang
>
>
>> Dear All,
>>
>> I am working on large dataset of two color arrays. For two color
>> arrays the normalizeBetweenArray function (limma) produces MAList from
>> RGList after normalization. My question is after normalization of two
>> color microarray data, whether arrayQualityMetrics should be run on M
>> (log ratios) matrix or A (average log intensity) matrix ? I am
>> guessing it should be run on A matrix as arrayQualityMetrics requires
>> matrix of microarray intensities to perform the analysis. But, I am
>> not sure. Any suggestion is appreciated.
>>
>> regards
>> Amit
>>
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>
> --
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
>
>