Moderator: t.kuilman

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t.kuilman100
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100
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Location:
Netherlands
Website:
https://github.com/Pee...
Last seen:
4 months, 3 weeks ago
Joined:
3 years, 4 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 • 36 results • page 1 of 4 • next >
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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 7 months ago by t.kuilman100
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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 11 months ago by t.kuilman100
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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 18 months ago by t.kuilman100
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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 19 months ago by t.kuilman100
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Comment: C: survcomp package - censor missing
... Awesome! I checked the help function of survcomp, but it only mentions that you can pass on additional parameters to the plot (and not plot.survfit) function. Thanks for this one :-) ...
written 20 months ago by t.kuilman100
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survcomp package - censor missing
... It seems that with the newest version of survcomp, the censor is missing (at least by default), as becomes clear from the vignettes. In version survcomp_1.18.0, the figure on page 20 of the vignette looks like this: However, in version survcomp_1.22.0, the corresponding figure looks like this: ...
survcomp written 20 months ago by t.kuilman100 • updated 20 months ago by shepherl ♦♦ 530
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Comment: C: CopywriteR can't finish calculating copy number
... Ok, I hope this solves the issue for you. Let me know how things go. ...
written 21 months ago by t.kuilman100
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Answer: A: CopywriteR can't finish calculating copy number
... Hi, To find out what is going on it would be very helpful if you could provide me with the exact commands / script you use to run CopywriteR, the exact common line output, the content of the CopywriteR.log file you find in your destination folder, and a sessionInfo(). One thing we have run into in ...
written 21 months ago by t.kuilman100
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Comment: C: Error using countBam (Rsamtools package)
... Thanks for clarifying that. Will it be implemented in the next Bioconductor release? ...
written 21 months ago by t.kuilman100
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Comment: C: Error using scanBam (Rsamtools package)
... Thanks for the suggestion. The maximum number an integer can have on my system is as follows: > .Machine$integer.max [1] 2147483647 Can any of the authors of the Rsamtools package fill us in whether counting reads can only go up to the maximum integer number? ...
written 21 months ago by t.kuilman100

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Scholar 2.1 years ago, created an answer that has been accepted. For A: Copyhelper: Preprocession of mappability
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