Question: arrayQualityMetrics - how do I use this with an MAList object???
gravatar for Park-Ng, Zaneta
10.2 years ago by
Park-Ng, Zaneta40 wrote:
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 AgResearch Limited Grasslands Research Centre Tennent Drive, Private Bag 11008, Palmerston North, New Zealand T +64 6 356 8019 F +64 6 351 8032 Farming Food and Health. First Te Ahuwhenua Te Kai me te Whai Ora. Tuatahi ====================================================================== = Attention: The information contained in this message and...{{dropped:15}}
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