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

[Marcus Davy]

Yes, looks like there is a problem with your version of the convert package
not being able to coerce an 'MAList' into an 'ExpressionSet'. However, I
think here you want to be coercing into an object instance of class
'NChannelSet'  as you have more than one channel on each slide.

>  showMethods("coerce", classes=c(from="RGList"))
Function: coerce (package methods)
from="RGList", to="NChannelSet"  # Can transform from an RGList only
from="RGList", to="marrayRaw"
from="marrayRaw", to="RGList"

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


You can backtransform an MAList into an RGList using 'RG.MA' to then coerce
into an NChannelSet.

>> x <- new("MAList")
>> x$M <- testRed
>> x$A <- testGreen
>> x$targets = testTarget
>> y <- as(x,"ExpressionSet")
>> z <- as(x,"NChannelSet")

z <- as(RG.MA(x), "NChannelSet")

arrayQualityMetrics(expressionset = z,
                          outdir = file.path("Metrics","z"),
                          force = TRUE,
                          do.logtransform = TRUE,
                          split.plots = FALSE,
                          intgroup = "RNAintegrity")


Incidentally I've noticed that the function plotMA in limma is masked by one
identically named from the package dependency 'beadarray' loaded by
'arrayQualityMetrics'.

> find("plotMA")
[1] "package:beadarray" "package:limma"

> limma::plotMA(x)
> X11()
> beadarray::plotMA(x)

This can cause some confusion as both functions are drawing similar MA
plots.


Marcus


On 13/9/08 1:41 AM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

> 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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