Moderator: t.kuilman

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t.kuilman140
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Posts by t.kuilman

<prev • 52 results • page 1 of 6 • next >
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GDCdownload error on CentOS 6.10 server
... I am trying to download data from TCGA using the TCGAbiolinks package. I have used the pet example from [the TCGAbiolinks Bioconductor-mirror](https://rdrr.io/github/Bioconductor-mirror/TCGAbiolinks/src/R/download.R), which works just fine on my Macbook, but throws an error on my server (CentOS 6.10 ...
tcgabiolinks written 6 days ago by t.kuilman140
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Answer: A: CopywriteR - should regions with very low coverage result in -1073741823.5?
... You are right that this represents a very low coverage. The output of CopywriteR is log2-transformed, and hence you would obtain -Inf if there is a coverage of 0. We replace those values by a (more or less randomly chosen) value of -.Machine$integer.max / 2 (i.e., the lowest possible integer value d ...
written 7 months ago by t.kuilman140
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Comment: C: One-sided p-value from DESeq2
... Fantastic, that's right what I need. Thanks for your quick reply; I should have spotted the altHypothesis argument of the results() function but apparently read past that. ...
written 7 months ago by t.kuilman140
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One-sided p-value from DESeq2
... For downstream analysis using a modified version of Robust Rank Aggregation (alpha-RRA; Li, et al. Genome Biology 2014), I would like to obtain one-tailed p-values from a standard DESeq2 analysis using a Wald test (rather than the two-tailed p-values that are represented in a 'DESeqResults' object). ...
deseq2 p-value nbinomwaldtest one-sided written 7 months ago by t.kuilman140 • updated 7 months ago by Michael Love23k
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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 8 months ago by t.kuilman140 • updated 8 months ago by Michael Love23k
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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 8 months ago by t.kuilman140 • updated 8 months ago by Michael Love23k
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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 10 months 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 months 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 10 months 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 10 months ago by t.kuilman140 • updated 10 months ago by Michael Love23k

Latest awards to t.kuilman

Scholar 3.3 years ago, created an answer that has been accepted. For A: Copyhelper: Preprocession of mappability
Autobiographer 4.1 years ago, has more than 80 characters in the information field of the user's profile.

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