[BioC] arrayQualityMetrics - how do I use this with an MAList object???

[Martin Morgan]

Hi Zaneta --

"Park-Ng, Zaneta" <Zaneta.Park-Ng at agresearch.co.nz> writes:

> Hi everyone,
>
> I'm trying to use the arrayQualityMetrics package on an MAList object,
> with no luck.  Does anyone know how to do this?  I can run the analysis
> fine on an RGList object, after first having converted this to an
> NChannelSet object, but am having problems with the MAList.  
>
> I've tried using the 'as' function from the convert package to try and
> create either an ExpressionSet or NChannelSet, but this fails, including
> on the test data given in the examples for "Convert Data Objects" using
> the Convert package.  The error message which I get is:  Error in as(x,
> "ExpressionSet") : 
>   no method or default for coercing "MAList" to "ExpressionSet"

The method exists in convert_1.16.0 which is the verion appropriate
for the current R release. After library(convert), what is the full
output of

> sessionInfo()

? Also, you should see

> showMethods("coerce", classes=c(from="MAList"))
Function: coerce (package methods)
from="MAList", to="ExpressionSet"
from="MAList", to="marrayNorm"
from="marrayNorm", to="MAList"

Perhaps you need to start a new sesssion of R and

> source('http://bioconductor.org/biocLite.R')
> update.packages(repos=biocinstallRepos())

?

> Where the code used for the test data is:
>
> library("convert")
> ##first set up some fake intensity matrices
> testRed = matrix(rnorm(5*2),5,2, 
>   dimnames=list(paste("gene",1:5, sep=""), c("S1", "S2")))
> testGreen = matrix(rnorm(5*2),5,2, 
>   dimnames=list(paste("gene",1:5, sep=""), c("S1", "S2")))
>
> ##some sample/target info
> testTarget = data.frame(slide=c("S1", "S2"), Cy3=c("T", "C"),
>   Cy5=c("C", "T"), row.names=c("S1", "S2"))
>
> x <- new("MAList")
> x$M <- testRed
> x$A <- testGreen
> x$targets = testTarget
> y <- as(x,"ExpressionSet")
> z <- as(x,"NChannelSet")
>
> And the code used for my real data is: 
>
> MA.QC <- as(MA, "ExpressionSet")
>
> Where note that MA was created using normalizeWithinArrays on an RGList
> object.
>
> I've also tried using normalizeWithinArrays on my raw data NChannelSet
> object, in case I could produce a normalized NChannelSet object in this
> way, but R also didn't like this...
>
> MA.NCh <- normalizeWithinArrays(RG.NChSet, method="printtiploess",
> bc.method="none")
>
> Error in MA.RG(object, bc.method = bc.method, offset = offset) : 
>   Object doesn't contain R and G components
>
> And now I'm stuck as to what to try next!!  Any ideas much appreciated
> :-)
>
> Note that I'm using: R version 2.7.0 (2008-04-22).  And
> arrayQualityMetrics_1.6.1
>
> Thanks very much for any help :-)
>
> Cheers,
> Zaneta
> ____________________________ 
> Zaneta Park 
> Biometrician 
> T +64 6 351 8008 
> E zaneta.park-ng at agresearch.co.nz 
> AgResearch Limited 
> Grasslands Research Centre 
> Tennent Drive, Private Bag 11008, Palmerston North, New Zealand 
> T  +64 6 356 8019   F  +64 6 351 8032  www.agresearch.co.nz 
> Farming Food and Health. First 
> Te Ahuwhenua Te Kai me te Whai Ora. Tuatahi 
>
>
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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