Moderator: t.kuilman

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t.kuilman140
Reputation:
140
Status:
Trusted
Location:
Netherlands
Website:
https://github.com/Pee...
Last seen:
1 week, 2 days ago
Joined:
3 years, 10 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 • 48 results • page 1 of 5 • next >
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Comment: C: DESeq2: handling NA values in colData
... Thanks for clarifying that. You mention in your previous mail that one should not use NA in colData, and use something like ‘missing’ instead; is there a specific reason for that? Best, Thomas ...
written 7 days ago by t.kuilman140 • updated 6 days ago by Michael Love19k
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DESeq2: handling NA values in colData
... In one of our studies we have performed RNAsequencing on a number of samples. I would like to compare to some of these in separate analyses using DESeq2, and the following design of the colData works fine for me: > sample <- factor(c("pos", "neg", "pos", "neg", NA, NA, NA, NA),             ...
deseq2 na coldata written 9 days ago by t.kuilman140 • updated 7 days ago by Michael Love19k
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Tutorial: Update gene symbols in GeneSetCollection
... I recently run into the problem that the gene annotation in MSigDB is not up to date (for example, the alias C14orf129 is used as a gene name in various gene sets, while the official HGNC symbol would be GSKIP). To fix this I have written a function to update all gene symbols:   alias.to.hgnc.gen ...
gseabase tutorial msigdb genesetcollection written 7 weeks ago by t.kuilman140
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Comment: C: DESeq2 design formula - correlation with ordered variable
... That was exactly what I was looking for, thank you very much! Just out of curiosity, you mention that one can use other mathematical functions. Is there for instance a rank-based method implemented in DESeq2 too? ...
written 10 weeks ago by t.kuilman140
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Comment: C: DESeq2 design formula - correlation with ordered variable
... I would like to find genes whose expression consistently decreases / increases with increasing sensitivity. Indeed, sensitivity would be treated as a numeric / ordered variable in this case. I am not sure I understand your question about functions, do you mean what kind of functions of DESeq2 I woul ...
written 11 weeks ago by t.kuilman140
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DESeq2 design formula - correlation with ordered variable
... I would like to analyse my RNAseq data using DESeq2, and have the following design: time.point cell.line sensitivity A_0 0 A 6 B_0 0 B 5 C_0 0 C 3 D_0 0 D 4 E_0 0 ...
deseq2 design formula matrix written 11 weeks ago by t.kuilman140 • updated 11 weeks ago by Michael Love19k
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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 3 months ago by t.kuilman140
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Comment: C: S4Vectors and subectHits error
... That is correct. Please let me know how things are going. ...
written 3 months ago by t.kuilman140
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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 3 months ago by t.kuilman140
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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 4 months ago by t.kuilman140

Latest awards to t.kuilman

Scholar 2.6 years ago, created an answer that has been accepted. For A: Copyhelper: Preprocession of mappability
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.

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