User: Jarno Tuimala

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Jarno Tuimala140
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Posts by Jarno Tuimala

<prev • 14 results • page 1 of 2 • next >
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Is anyone developing an extensible Galaxy-like interface for Bioconductor?
... Hello! We have developed, and continue to develop Chipster, a graphical user interphase build on top of R and Bioconductor. It is currently steered mostly towards DNA microarray data analysis, but it can be easily extended with any R function, Java code or command line tool. Chipster is a client-s ...
affylmgui limmagui written 10.2 years ago by Jarno Tuimala140 • updated 10.2 years ago by Ross Lazarus90
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Answer: A: Changing margins on a boxplot
... Hi! You can set margins to boxplot (or any plot for that matter) by first setting the graphical parameters, e.g.: par(mar=c(0,0,0,0)) # Removes margins par(mar=c(5,4,4,2)+0.1) # Default par(mar=c(8,8,4,2)) # Larger bottom and left margins and then calling the boxplot function: boxplot(rn ...
written 10.5 years ago by Jarno Tuimala140
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Comment: C: Help on Loading AgilentData into LIMMA
... Hi Wendy! > No my files were not created with a genePix program. My raw data were > obtained with agilent's Feature extraction. That was why I was using > source="agilent" Sorry, my mistake! > I thought F635 and F532 were codes to imply foreground and background but I > guess I was ...
written 10.5 years ago by Jarno Tuimala140
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Answer: A: Help on Loading AgilentData into LIMMA
... Hello! > RG<-read.maimages("targets.txt", source="agilent", > columns=list(gBGMeanSignal="F635", gBGMeanSignal="F532", > bBGMedianSignal="B635 Median", bBGMedianSignal="B532 Median"), > annotation=c("Block", "Column", "Row", "Name", "ID")) You seem to have a datafile that has been c ...
written 10.5 years ago by Jarno Tuimala140
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Comment: C: Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under
... Hi! The methodology of generating these remapped probes packages is described in NAR, and on the the web. See: http://nar.oxfordjournals.org/cgi/content/full/33/20/e175 http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf readme.htm There is also an example of how to use these p ...
written 11.0 years ago by Jarno Tuimala140
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Answer: A: ctc package - cluster dendrogram
... Hi! If you draw a dendrogram in R, the y-axis is the distance between objects. In your case, the tree looks roughly like: 4 +--+ | | | 3 1 | | +-+ 2 | | 2 3 As the branch which connects V2 and V3 is at approx. 2.4 it is the distance between these objects (samples). The same appli ...
written 11.0 years ago by Jarno Tuimala140
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Answer: A: problems with command "download.file"
... Hi! You probably need to download the file in binary mode. Try: download.file(url="http://bloodjournal.hematologylibrary.org/cgi/repri nt/102/7/2345.pdf",destfile="dest.pdf", mode="wb") Regards, Jarno On Mon, 10 Sep 2007, Li Lingdu wrote: > Hello R-gurus, > > I am using R command "do ...
written 11.1 years ago by Jarno Tuimala140
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Answer: A: Removing libraries or using a particular function
... Hi! A package can be unloaded using the detach-command: detach(package:DNAcopy) or detach(package:tilingArray) Regards, Jarno On Tue, 17 Jul 2007, Daniel Brewer wrote: > Hello, > > Another quick question that I am sure is answered somewhere on the net, > but I have been unable t ...
written 11.3 years ago by Jarno Tuimala140
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Answer: A: displayTIFFImage funtion in beadarray package
... Hi! It would seem that the function displayTIFFImage has not been exported from the namespace of beadarray. But, you can still access the function by using the notation: beadarray:::displayTIFFImage() Regards, Jarno On Thu, 12 Jul 2007, Sebastien Gerega wrote: > Hi, > I am trying to use ...
written 11.3 years ago by Jarno Tuimala140
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Comment: C: linkage distances
... Dear Daniel, Package ape in CRAN contains functions one can use for calculating a consensus of several dendrograms (consensus). Consensus function can produce either a strict or majority rule consensus. Strict consensus contains only the groups that are present in all the trees, whereas majority ru ...
written 11.4 years ago by Jarno Tuimala140

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