User: Marcus Davy

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Marcus Davy680
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Posts by Marcus Davy

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Masking of limma objects by beadarray when loading arrayQualityMetrics
... Hi, I just wanted to make a note of a small issue that if you use 'limma' combined with 'arrayQualityMetrics' there is a masking of some functions caused by the loaded package dependency 'beadarray'. # Doesn't matter which way around packages are declared 'beadarray' seems to # be higher in the sea ...
written 10.4 years ago by Marcus Davy680 • updated 10.4 years ago by Mark Dunning50
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Answer: A: arrayQualityMetrics - how do I use this with an MAList object???
... 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( ...
written 10.7 years ago by Marcus Davy680
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Comment: C: limma: cannot repoduce older analysis
... Additional to the points mentioned, you can check the log of changes to limma, e.g. changeLog(n=200) To determine what functions may have changed in the time period. When comparing your analysis from a reproducible research point of view if you have any old objects stored (saved R session or obje ...
written 10.8 years ago by Marcus Davy680
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ArrayQuality package bug in agQuality function - marray package
... Hi, there appears to be a bug in the arrayQuality package, specifically the agQuality function which traces back to the function read.Agilent in the marray package. If I specify a path for the location of Agilent microarray files to process which is not the current working directory (path=".", and ...
microarray arrayquality written 10.9 years ago by Marcus Davy680
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Answer: A: topTable threshold on p-value and logFC [Re: was design matrix]
... Condensed function for filtering based on Martins suggestions; ttFilter <- function( filter = "abs(logFC) > 0.69 & abs(t) > 2", fit, sort.by="t", number = nrow(fit), ...) { tt <- topTable(fit, sort.by = sort.by, number = number, ...) # Obtain logical from filter toSub &l ...
written 11.6 years ago by Marcus Davy680
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Answer: A: topTable threshold on p-value and logFC [Re: was design matrix]
... Thanks for the information. Yes you are correct, the code; >> if( any(is.na(toSub)) ){ >> toSub <- toSub[!is.na(toSub)] >> } >> return(tt[toSub, ]) is a bug and needs to be removed because of recycling it will stuff the returned index up. That was a quick hack ...
written 11.6 years ago by Marcus Davy680
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topTable threshold on p-value and logFC [Re: was design matrix]
... Additionally to decideTests(), I made a function which is useful for making *any* filter you like. The example provided filters the same as decideTests(). You must correctly specify the columns of interest in the ''filter'' expression argument so some knowledge of limma's data structures is required ...
written 11.6 years ago by Marcus Davy680
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Comment: C: how to revert to an older limma version?
... Also if installing a previous version check in R that it is installed with sessionInfo(). You might want to check the changeLog(n=100) to see if readGenericHeader has been changed in recent package releases. You can obtain some old archived releases at; http://bioinf.wehi.edu.au/limma/ and htt ...
written 11.9 years ago by Marcus Davy680
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"AveExp" column has dissappeared from limma topTable
... Have a look in your 'fit' object and the lmFit code for clues as to what is going wrong. When you create a fit object from lmFit, a list element called 'Amean' may not have been created. This is what is picked up by topTable. You didn't mention the structure of the argument object 'Mosquito' in y ...
go survival annotate geneplotter affydata limma annaffy affyplm written 12.2 years ago by Marcus Davy680 • updated 12.1 years ago by Gordon Smyth37k
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Error in RankProd package
... Error in RankProd package, specifically related to the RP and topGene functions and the way RP, handles missing values for an entire row of observations for a gene. Filtering out rows of missing values will get around this. The help(RP) documentation provides the following information about NA ha ...
limma rankprod written 12.2 years ago by Marcus Davy680 • updated 12.2 years ago by Gunther Höning100

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