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"

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@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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