User: Oosting, J. PATH

Reputation:
550
Status:
Trusted
Location:
Last seen:
7 years, 2 months ago
Joined:
15 years, 7 months ago
Email:
j********@lumc.nl

Posts by Oosting, J. PATH

<prev • 55 results • page 1 of 6 • next >
0
votes
1
answer
1.4k
views
1
answers
Comment: C: genotyping output files
... As I had this requirement just the other week with affy SNP 6 arrays, I made a small script to produce map and ped files. You probably need some changes for your particular situation , like selecting the correct columns from an annotation file. targets is a dataframe containing patient information. ...
written 7.2 years ago by Oosting, J. PATH550
0
votes
2
answers
553
views
2
answers
Answer: A: question subsetting expressionSet
... An alternative would be to read in your phenodata with as.is=TRUE. Then all variables in the dataframe will be vectors. You can generate the factors when you need them ie. When constructing a model for the analysis. pheno <- read.delim(file="A213_metadata.txt", row.names=1,as.is=TRUE) Jan I t ...
written 7.2 years ago by Oosting, J. PATH550
0
votes
1
answer
705
views
1
answers
Answer: A: plotting probes along a chromosome
... A similar question with a number of possible solutions can be found on BioStar http://biostar.stackexchange.com/questions/378/drawing-chromosome- ideogams-with-data/ Jan ________________________________________ Hello List, I am trying to graph the position of probes ~50 nucleotides in length alon ...
written 7.7 years ago by Oosting, J. PATH550
0
votes
1
answer
645
views
1
answers
Answer: A: karyotype annotation
... You mean something like this: library(quantsmooth) chrom=16 plot(1,xlim=c(0,lengthChromosome(chrom,"bases")), ylim=c(0,4),type="n",xaxt="n",yaxt="n", xlab="",ylab="",main="chromosome 16") paintCytobands(chrom, pos = c(0, 3.5), units = "bases", width = 0.4) text(c(20944476,83841592),c(2,2) ...
written 7.9 years ago by Oosting, J. PATH550
0
votes
1
answer
557
views
1
answers
Answer: A: karyotype annotation
... The quantsmooth package has a position2cytoband() function you could use Jan > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r- > project.org] On Behalf Of Nandini B > Sent: dinsdag 19 april 2011 15:18 > To: bioconductor at ...
written 7.9 years ago by Oosting, J. PATH550
0
votes
1
answer
518
views
1
answers
Answer: A: Illumina human ht12 v3 beadchip and illuminaHumanv3BeadID.db
... This is normal for this chiptype. The HT12 contains a lot of probes that have no proper annotation. These are mostly ESTs that have been submitted to Genbank at some time, but have never been properly attributed to any gene. For most types of analysis these extra probes are basically worthless, so ...
written 8.3 years ago by Oosting, J. PATH550
0
votes
2
answers
743
views
2
answers
Answer: A: Circular binary segmentation for allele-specific CN data
... The problem with segmenting fracB data is that it does not behave as a certain value + noise in segments. This violates the assumption for any segmentation algorithm. In normal samples neighboring SNPs can have fracB values of 0 (for AA genotype), 0.5 (AB) or 1 (BB). In the ideal situation you can f ...
written 8.6 years ago by Oosting, J. PATH550
0
votes
3
answers
532
views
3
answers
Answer: A: plotting multiple genes on a genome
... The prepareGenomePlot() function in the quantsmooth package can be used to do that. Jan ________________________________ Hello, I would like to plot a list of interesting genes (located on different chromosomes) on a genome. I extracted their genomic coordinates with biomaRt (see table below) a ...
written 9.4 years ago by Oosting, J. PATH550
0
votes
1
answer
658
views
1
answers
Comment: C: limma for identifying differentially expressed genes from illumina data
... With Illumina arrays I usually filter out all the un-annotated probes before doing the statistical analysis. Especially in the 48k versions of these arrays about half the probes are not annotated, and for most purposes these are not interesting. Furthermore you should have a look at the quality of ...
written 9.6 years ago by Oosting, J. PATH550
0
votes
1
answer
364
views
1
answers
Answer: A: How to run bioHMM on Affymetrix data?
... You will have to create a SegList object in order to do this, for the runBioHMM() function a SegList needs to have the following components M.observed: a matrix with the copynumber values samples in columns, probes in rows genes: A data.frame with at list a Chr and a Position column Make sure that ...
written 9.9 years ago by Oosting, J. PATH550

Latest awards to Oosting, J. PATH

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 342 users visited in the last hour