User: Oosting, J. PATH

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Posts by Oosting, J. PATH

<prev • 55 results • page 2 of 6 • next >
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Answer: A: How to display chromosome rapresentation ?
... Hi Giulio, The paintCytobands() function of the quantsmooth package gives nice pictures of chromosomes. Also the idiogram and geneplotter packages help in visualizing genomic information. Jan > > > I have several results of a CGH analysis, where a statistic is plotted > vs the chromoso ...
written 10.2 years ago by Oosting, J. PATH550
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Comment: C: Heatmap problem
... By using the triple colon you can use objects/functions that are not exported from the namespace. i.e. annotate:::getQuery4Affy() Jan > Is there no way to call a user function from a namespaced package? > ...
written 10.4 years ago by Oosting, J. PATH550
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Postdoctoral Bioinformatics position available at the Leiden University Medical Centre
... For the project 'Automated integrated analysis of genotype and allele-specific copy number abnormalities in non-homogeneous solid malignant tumors' we have a vacancy for a post doctoral researcher in Bioinformatics. Part of the part is to extend the Bioconductor beadarraySNP package. More informati ...
written 10.6 years ago by Oosting, J. PATH550
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Answer: A: Processing data from Illumina HumanCNV370-Quad chips
... Hi Steven, If you have access to Beadstudio, probably the easiest way to get Illumina SNP data loaded in beadarraySNP is the following - Do genotyping of your data in Beadstudio - Create a final report (From the Analysis->Reports menu) that contains at least the fields 'SNP Name', 'Sample ID', ' ...
written 10.6 years ago by Oosting, J. PATH550
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Answer: A: Need help using read.table to read in non-standard data
... You should take a look at the limma analysis of affymetrix and other single-channel designs, as this is what you have now basically. The examples in the userguide on this type of data do not need a targets.txt file. Jan > I have a question about reading in data for use with the Limma package by ...
written 10.7 years ago by Oosting, J. PATH550
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Comment: C: gains and losses via mode shifting
... > From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- > bounces at stat.math.ethz.ch] On Behalf Of Benjamin Otto > Sent: maandag 30 juni 2008 14:09 > I was hoping there would be a solution, which incorporates some global > information about all samples. Suppose I w ...
written 11.0 years ago by Oosting, J. PATH550
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Answer: A: karyogram
... You may have a look at the quantsmooth package, which has a function prepareGenomePlot() that can draw all idiagrams of a genome, and the functions grid.chromosome() and plotChromosome() that can plot ideograms at any location within a plot. Jan > -----Original Message----- > From: bioconduc ...
written 11.0 years ago by Oosting, J. PATH550
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Answer: A: Question - Merged Arrays and Averaging Method
... > I am a new user of the Bioconductor suite and have a question for the > list. When performing an analysis, since I have duplicate arrays, I am > merging my duplicate arrays before normalizing my data. I have an option > to use the mean or median values and also to log2 transform my d ...
written 11.4 years ago by Oosting, J. PATH550
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Answer: A: beadarray bead-level normalisation for single channel data
... I have also thought about between array quantile normalization for bead arrays, but the implementation is not straightforward because the arrays have different numbers of (reported) beads. For quantile normalization it will probably be necessary to pad the arrays with smaller amounts of beads, where ...
written 11.8 years ago by Oosting, J. PATH550
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Answer: A: How to sort a matrix based on its column names and preserving the identical colu
... mat<-mat[,order(colnames(mat))] Jan > How to sort a matrix based on its column names and preserving the > identical column names. > > when I use mat [, sort(colnames(mat))], sort changes all column names to > unique ones. for ex, if the name of 2 columns is col, the 2nd will be ...
written 11.9 years ago by Oosting, J. PATH550

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