User: Marcus Davy

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Marcus Davy680
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Posts by Marcus Davy

<prev • 68 results • page 3 of 7 • next >
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Comment: C: limma: read.maimages possibility to warn the user?
... Hi, member[2] - member[3] is going to give an error os the binary operator "-" cannot operate on strings, > member[2] - member[3] Error in member[2] - member[3] : non-numeric argument to binary operator try, design <- diag(3)[rep(1:3, each=2),] colnames(design) <- member member <- LE ...
written 13.0 years ago by Marcus Davy680
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Answer: A: Dist of exprSet object
... P 17 of the vignette("affy"). e.g. chipCols <- rainbow(ncol(exprs(affybatch.example))) boxplot(affybatch.example, col=chipCols) Marcus On 7/27/06 10:40 AM, "Marco Blanchette" wrote: > Thank you all, > > Using bioclite to download the annotation fixed the problem. > > Now, I ...
written 13.0 years ago by Marcus Davy680
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Comment: C: marray and gathering additional information from GenePix GPR file
... Yes the spot intensities (labeled "Empty") which are recorded in a GenePix gpr file should be distributed similarly to the background intensities on a 16 bit GenePix scanner (between 0 and several hundred). Essentially they are measures of background in the foreground spot area. Yes I mean A value ...
written 13.0 years ago by Marcus Davy680
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Comment: C: marray and gathering additional information from GenePix GPR file
... Just to add further comment to this discussion about empty spots in GenePix. Empty spots could be due to the physical printing not taking place at that spot position or buffer which contains no physical cDNA/oligo probe could be deposited by the printing quill at that spot position. In gpr files ...
written 13.0 years ago by Marcus Davy680
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Answer: A: default BG subtraction in plotMA...
... Hi, Default function arguements in limma use background subtraction of information (Section 6.1 p20, 20-Apr-2006 edition). I guess more clarity could go into the help pages for plotMA and plotMa3by2 themselves ( This applies to plotPrintTipLoess aswell). A simple way to change the behaviour is to ...
written 13.2 years ago by Marcus Davy680
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Answer: A: Targets file, array labels and Limma versions
... Jenny, help(readTargets) mentions that If 'row.names' is null, then the column 'Labels' will be used if such exists or, failing that, the column 'FileName'. This looks like a small typo as the column has to be "Label" not "Labels" in ReadTargets <- function(){ ... if ("Label" %in% names( ...
written 13.6 years ago by Marcus Davy680
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Answer: A: hexbin in R 2.2.0 - installation problem
... The colorspace dependency is available from any cran mirror, e.g. http://cran.au.r-project.org/src/contrib/Descriptions/colorspace.html Marcus On 10/20/05 7:58 AM, "Naomi Altman" wrote: > I just downloaded R 2.2.0 for Windows, after which I installed > several Bioconductor packages using ...
written 13.8 years ago by Marcus Davy680
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Answer: A: problem normalizeMedians (limma)
... Hi, Doe this include modifying normalizeMedianDeviations aswell for consistency. I suspect normalizeMedianDeviations doesn't reach R's limit as quickly. Marcus MA <- new("RGList") n <- 200 genes <- 1000 MA$M <- matrix(runif(n*genes, -8, 8), nr=genes, nc=n) MA$A <- matrix(run ...
written 13.8 years ago by Marcus Davy680
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Answer: A: ReadAffy(widget=TRUE) on OSX 10.4
... Hi, I am getting the exact same problem on a fresh install of OS X 10.4 on a G5 patched to 10.4.2 . On starting the R.app, and starting X11, and running the commands; library(affy) ReadAffy(widget=T) I hear the CPU fans kick in and the R.app and tcltk window becomes non responsive. This also hap ...
written 13.9 years ago by Marcus Davy680
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normalizing incomplete arrays [was: limma errormessage]
... you can use the function RG.MA to convert your M and A values back into normalized R and G values. > RG.MA function (object) { object$R <- 2^(object$A + object$M/2) object$G <- 2^(object$A - object$M/2) object$M <- NULL object$A <- NULL new("RGList", unclass(obje ...
normalization limma convert written 14.0 years ago by Marcus Davy680 • updated 14.0 years ago by Jianping Jin890

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