Dear Amit,

Apparently the sampleNames are not the same in your assayData and in your
phenoData, you should carefully check this first.
The expressionSet should contain the M values.
For the conversion, you can try:
 new("ExpressionSet",exprs=rat_norm_MA$M)

Best wishes,
Audrey


-- 
Audrey Kauffmann
Bergonie Cancer Institute
229 Cours de l'Argonne
33076 Bordeaux
France
+33.5.56.33.04.53


2010/4/15 Amit <amitkumartiwary@gmail.com>

> 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@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
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > --
> >
> >
> > Wolfgang Huber
> > EMBL
> > http://www.embl.de/research/units/genome_biology/huber
> >
> >
> >
>
> _______________________________________________
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>

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