User: Rik Verdonck

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Rik Verdonck40
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1 year, 9 months ago
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r***********@bio.kuleuven.be

Posts by Rik Verdonck

<prev • 6 results • page 1 of 1 • next >
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Answer: A: kallisto/sleuth for single sample pathway enrichment
... Hi Endre, As an answer to your **first question**: it depends on what you want to know. If your individual mutated samples are of interest to you, then you should certainly compare them to your best guess of a normal expression pattern (i.e. some kind of mean or median of your controls). If, howe ...
written 3 months ago by Rik Verdonck40
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Comment: C: EBSeq explained to a biologist
... Thanks for your suggestions. I highlighted my questions. This is not a tutorial indeed, but what I hope is that, based on comments/amendments of the community, I will be able to re-write the text into a correct and reasonably complete explanation of the inference framework that underlies this packa ...
written 18 months ago by Rik Verdonck40
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EBSeq explained to a biologist
... **Disclaimer 1: I also posted this in the [EBSeq google group][1], but it does not seem to attract much attention.** **Disclaimer 2: this is a long post, but I think it is well worth reading and answering to for people (like me) who really want to understand how EBSeq works, but did not get there b ...
R ebseq rna-seq written 18 months ago by Rik Verdonck40
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Answer: A: Help understanding patterns in EBSeq
... It's all about testing which hypothesis best describes the data that you see. Say you have 3 conditions: male, female and hermaphrodite. Then `1 1 1` fits those genes for which there is no sex effect, `1 2 2` are those genes that have similar expression between females and hermaphrodites, but differ ...
written 18 months ago by Rik Verdonck40
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Some questions about bayseq DE
... Hello everybody, I'm currently analyzing a set of 30 samples (6 conditions, 5 replicates each) in bioconductor bayseq. I mapped the 30 sets of +- 20M 50bp SE illumina reads against 23321 reference sequences that were pre-selected from a *de-novo* assembled transcriptome. This selection of contigs ...
bayseq R bioconductor next-gen rna-seq written 21 months ago by Rik Verdonck40 • updated 20 months ago by tjh4820
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Answer: A: errors from evidentialgene pipeline
... For what it's worth five months later: I came across similar errors, and had a hard time figuring out what was happening because the error message by cd-hit was nothing more than their help page. In the end, I figured it was the multi-threading that went wrong. If you are running a cd-hit version ...
written 21 months ago by Rik Verdonck40

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