User: Martin Rijlaarsdam

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Posts by Martin Rijlaarsdam

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Answer: A: non specific filtering 27k methlylation chip
... Hi, I would think so (at least I did it with 450 K data). Or just apply your method of choice for variance filtering (IQR or sd) to each probe and filter out your percentage of choice. Maybe plot a histogram of the variance measure to see it's distribution and see if there exists a logical cutoff. ...
written 5.5 years ago by Martin Rijlaarsdam190
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Comment: C: QQ plot 450k data
... Hi Jim, Jim, if (groups) of samples differ in their global methylation profile (i.e. the majority of probes significantly differs in one direction), would you not expect to see a deviation from this uniform distribution then? Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - Univers ...
written 5.6 years ago by Martin Rijlaarsdam190
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Comment: C: gviz data track (heatmap) and title panel questions
... Dear Florian, Thank you. Will you also implement this (small) bugfix in the release branch? Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands V ...
written 5.6 years ago by Martin Rijlaarsdam190
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Comment: C: gviz data track (heatmap) and title panel questions
... ... and if I set col.title = "black" in specific track the same thing happens (black box around title panel) but now only for that specific track. Tnx! Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress ...
written 5.6 years ago by Martin Rijlaarsdam190
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Comment: C: gviz data track (heatmap) and title panel questions
... Dear Florian, Can I ask one more dummy question. When I add " col.title="black" " to the plotTracks parameter list, a black box appears around all title panels. Setting col.border.title="white" and/or lwd.border.title=0 does not help. I would prefer not to show any lines around the title panels. T ...
written 5.6 years ago by Martin Rijlaarsdam190
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Comment: C: gviz data track (heatmap) and title panel questions
... Hi, Thanks a lot. Turns out I was using an outdated version of Gviz without that feature. Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Vis ...
written 5.6 years ago by Martin Rijlaarsdam190
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Comment: C: Fwd: adjusted P-values
... Dear Tim, Thank you for your reply. In my reply I was merely pointing out that Kaushals' original question, could be better answered if (more) information about the samples/sample size and the analysis pipeline would have been provided. In response, however, my answer might have also been too shor ...
written 5.6 years ago by Martin Rijlaarsdam190
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Fwd: adjusted P-values
... Hi, Highly variable probes are not necessarily differentiating between groups (if that is what you are aiming at). Please give some more information about your experiment and what tool / procedure you use for testing and correction for multiple testing. Also look at Wilhelm-Benartzi CS, Koestler D ...
cancer genefilter written 5.6 years ago by Martin Rijlaarsdam190 • updated 5.6 years ago by Tim Triche4.2k
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Answer: A: gviz data track (heatmap) and title panel questions
... PS I know about the showAxis=F settings, but if I do that, my sample names disappear as well... Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands ...
written 5.6 years ago by Martin Rijlaarsdam190
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gviz data track (heatmap) and title panel questions
... Dear Sirs, Thank you very much for Gviz! I have been using it for a while now but I have two issues that I cannot seem to figure out. Both are pretty trivial settings, so my apologies in advance. Please see the attached image as an example. 1) I would like to rotate the text in the title panel ...
written 5.6 years ago by Martin Rijlaarsdam190 • updated 5.6 years ago by florian.hahne@novartis.com1.6k

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Popular Question 5.5 years ago, created a question with more than 1,000 views. For gviz data track (heatmap) and title panel questions

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