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:
2 months ago
Joined:
2 years, 3 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 • 34 results • page 1 of 4 • next >
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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 ...
rna-seq gsva preprocessing rnaseq written 5 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 5 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 7 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 7 months ago by t.kuilman100 • updated 7 months ago by shepherl ♦♦ 130
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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 7 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 7 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 7 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 7 months ago by t.kuilman100
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Error using countBam (Rsamtools package)
... I have run a very large bam (186 G) file through the countBam function from the Rsamtools package, and got an unexpected error: > library(Rsamtools) > countBam(large.bam.file) Error in value[[3L]](cond) : 'countBam' failed: record: -2023186199 error: 0 file: /home/NFS/research_projec ...
countbam rsamtools written 7 months ago by t.kuilman100
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Comment: C: Preparing CopywriteR output for GISTIC 2.0 analysis
... Thanks for pointing that out, I will adjust the original answer to incorporate your comment. ...
written 10 months ago by t.kuilman100

Latest awards to t.kuilman

Scholar 12 months ago, created an answer that has been accepted. For A: Copyhelper: Preprocession of mappability
Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.

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