Entering edit mode
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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