Moderator: t.kuilman

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t.kuilman130
Reputation:
130
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Trusted
Location:
Netherlands
Website:
https://github.com/Pee...
Last seen:
18 hours ago
Joined:
3 years, 6 months ago
Email:
t********@nki.nl

I am a postdoctoral fellow at the Netherlands Cancer Institute focussing on both biological and bioinformatic approaches to understand cancer drug responses.

Posts by t.kuilman

<prev • 42 results • page 1 of 5 • next >
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Comment: C: S4Vectors and subectHits error
... Yes, in principle you should get the same error even if you re-run your samples with the updated sample.control variable. What this error means is that the calculations of the loesses (GC-content ~ read counts and mappability ~ read counts) failed. The reason for this is usually that there are not e ...
written 5 days ago by t.kuilman130
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Comment: C: S4Vectors and subectHits error
... That is correct. Please let me know how things are going. ...
written 5 days ago by t.kuilman130
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Comment: C: S4Vectors and subectHits error
... I got your mail with the CopywriteR.log file. It struck me that the sample.control argument that you are using is not correct. Please refer to this website on the CopywriteR Github page ...
written 5 days ago by t.kuilman130
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Comment: C: S4Vectors and subectHits error
... I run two samples in a way that would have caused the bug to throw an error message in older versions of CopywriteR, but with both version 2.8.1 and 2.10.0 it run without problems. I could not find 2.9.0, which happens to be a development-version of CopywriteR. Could you try updating to 2.10.0 and r ...
written 6 days ago by t.kuilman130
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Comment: C: S4Vectors and subectHits error
... Ok, that is indeed a known bug but as far as I am aware it should be fixed as of version 2.8.1. I am currently testing a few CopywriteR versions (including 2.9.0) to see whether this bug still occurs. Will keep you updated... ...
written 6 days ago by t.kuilman130
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Comment: C: S4Vectors and subectHits error
... Indeed, our CopywriteR package does depend on subjectHits, but since a small test sample is run during building for the vignette, all the dependencies should be fine. Is it possible to install CopywriteR again using the biocLite tool: > source("https://bioconductor.org/biocLite.R") > biocLit ...
written 6 days ago by t.kuilman130
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Answer: A: BiocParallel and CopywriteR Error
... I am not sure whether this is an issue with CopywriteR; I think this might be an issue with BiocParallel (the package in which the bplapply function is specified) and/or an memory issue. I hope someone else can help with this issue. ...
written 9 months ago by t.kuilman130
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Answer: A: Problems with CopywriteR
... I have not seen this error message before, but there is nothing wrong with the code you provide. Nevertheless, it would be helpful if you could provide all the code you used to run CopywriteR, as well as the CopywriteR.log file that is in the output. Also, in the mean time, can you try the following ...
written 13 months ago by t.kuilman130
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Pre-processing of RNA sequencing data for GSVA
... I would like to run gene set variance analysis (GSVA) on RNA sequencing data using the GSVA package, but I am confused as to what kind of input I am supposed to use for these analyses. In the vignette, an eset (pickrellCountsArgonneCQNcommon_eset) is used as input for the gsva() function: > hea ...
rnaseq preprocessing gsva rna-seq written 20 months ago by t.kuilman130
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Answer: A: CNV calling on normals samples / gaps in chromosomes
... Regarding your question about analysing the normal sample: I would not expect any amplifications (copy number alterations), but only (germline) copy number variations. The CopywriteR tool is written for detection of copy number alterations (for instance in tumor material), and it filters out CNV reg ...
written 21 months ago by t.kuilman130

Latest awards to t.kuilman

Scholar 2.3 years ago, created an answer that has been accepted. For A: Copyhelper: Preprocession of mappability
Autobiographer 3.1 years ago, has more than 80 characters in the information field of the user's profile.

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