Question: arrayQualityMetrics - how do I use this with an MAList object???
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gravatar for Martin Morgan
10.8 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k 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 > > > > ==================================================================== === > Attention: The information contained in this message and...{{dropped:15}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
ADD COMMENTlink modified 10.8 years ago by Marcus Davy680 • written 10.8 years ago by Martin Morgan ♦♦ 23k
Answer: arrayQualityMetrics - how do I use this with an MAList object???
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gravatar for Marcus Davy
10.8 years ago by
Marcus Davy680
Marcus Davy680 wrote:
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 <- asRG.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 >> >> >> >> =================================================================== ==== >> Attention: The information contained in this message and...{{dropped:15}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor The contents of this e-mail are privileged and/or confid...{{dropped:5}}
ADD COMMENTlink written 10.8 years ago by Marcus Davy680
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