User: Marcus Davy

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Marcus Davy680
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Posts by Marcus Davy

<prev • 68 results • page 2 of 7 • next >
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Answer: A: Gene density plot with points underneath
... Daniel, You can use the lattice package to create conditioned density plots with a dataframe as input and a model formula, e.g. library(lattice) densityplot(~height, data=singer) A first principles approach would be to create a density plot with enough room to be able to add the expression point ...
written 12.1 years ago by Marcus Davy680
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Answer: A: limma, spot quality weight
... Try modfying your statement x[,"FlagA"]="A"|"B"|"C" etc to use the test operator rather than the assignment operator. Something like; okred <- x[,"FlagA"]=="A" | x[,"FlagA"]=="B" | x[,"FlagA"]=="C" Marcus On 12/1/06 8:52 AM, "Yolande Tra" wrote: > Hi, > > I have cDNA array data p ...
written 12.4 years ago by Marcus Davy680
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Comment: C: limma
... It would be better to replace the unwanted elements with NA's rather than subset the structure, imageplot's for example will not work if the subsetted RGList or MAList is incomplete. e.g. MA$M[select,] <- NA Marcus On 11/28/06 6:19 AM, "Naomi Altman" wrote: > I usually do this using a ...
written 12.4 years ago by Marcus Davy680
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Answer: A: PC/Mac version-checking inside of R
... Use, R.version (or type version), and .Platform, and sessionInfo() Is useful too Marcus On 9/15/06 10:48 AM, "Simon Lin" wrote: > Is there a function to determine which version of R you are running? > > For example, quartz() will work on Macs, but not on Windows. > > Thanks! & ...
written 12.6 years ago by Marcus Davy680
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Comment: C: X11 problem
... This came up on a thread recently regarding the OS X operating system where the exact same error message occurred. You need to install X11R6 or X11R7 on fedora to allow R to interface with X11 and produce X11, png, or jpeg graphics. After installing X11R6/7 I would then build R from source again. ...
written 12.6 years ago by Marcus Davy680
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Answer: A: maQualityPlots on Mac
... Details on the second possibility, http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#TclTk-issues There was a typo in the function name, it is supposed to be '.First' . Marcus ----- Have you installed the X11.app from the tiger/panther installation disks? The X11.app needs to be running ...
written 12.6 years ago by Marcus Davy680
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Answer: A: maQualityPlots on Mac
... Have you installed the X11.app from the tiger/panther installation disks? The X11.app needs to be running in conjunction with R to then access the X11 graphics. I believe quartz() doesn't need X11.app to work. Also, I make a Rprofile.site file to store global options in R_HOME$/etc, For a system ...
written 12.6 years ago by Marcus Davy680
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Answer: A: readGenericHeader problem in limma 2.7.8?
... Relating to your question, > I don't know how to attempt an install of 1.7 to see if that affects > anything. You want to use limma which does not have any critical package dependencies so you don't need BioC 1.7 unless you want to use other classes and methods than that provided in limma. ...
written 12.7 years ago by Marcus Davy680
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Comment: C: How to create a MAList or ExprSet object from a matrix
... Further to Martin's email, this code might be useful to you for what looks like your probe set information after normalization. Marcus tmp <- scan(what=character(0)) 56071 1052 1062 3061 3081 8052 8072 10061 10062 10072 1415670_at 8.430148 8.899385 8.625973 8.708319 8.759182 8.281378 8.905347 ...
written 12.7 years ago by Marcus Davy680
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Answer: A: exclude flagged spots in limma
... Here are a few of ways; > x [1] 0 1 0 0 1 > (!x)*1 [1] 1 0 1 1 0 > as.numeric(!x) [1] 1 0 1 1 0 > abs(x - 1) [1] 1 0 1 1 0 The logical operator "!" coerces the binary vector to logical and does a logical negation (NOT). A weight of 0 is equivalent to an NA, a weight between 0 and ...
written 12.7 years ago by Marcus Davy680

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