User: b.nota

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b.nota330
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330
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Netherlands
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2 weeks ago
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4 years, 7 months ago
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Posts by b.nota

<prev • 143 results • page 2 of 15 • next >
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Comment: C: What does "level" argument mean in groupGO function (cluster profiler)?
... Thanks for your comment. So due to the complexity of the GO graph structure, it is probably not possible to find a level where all GO terms are given. I didn't realize it, thanks for your time. ...
written 17 months ago by b.nota330
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Comment: C: What does "level" argument mean in groupGO function (cluster profiler)?
... Thanks again, I understand what you mean. Sorry I gave you that impression. I was actually not asking about a simple hypergeometric test, I understand how to do that with this package. I thought I was clear about that in my question, but probably I was not. I was interested in getting all GO terms, ...
written 17 months ago by b.nota330
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Comment: C: What does "level" argument mean in groupGO function (cluster profiler)?
... Thanks for your comment James, and yes I have read the vignette but still can't figure out how level should be set to get all the terms, or how it is possible that the number of terms decreases with very high level. I don't completely understand your irritation, because I don't understand why I giv ...
written 17 months ago by b.nota330
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Comment: C: What does "level" argument mean in groupGO function (cluster profiler)?
... Thanks for the explanation and example. So how do I get all GO terms for all levels? If you look at my examples, you'll see that with level = 15 (and 20) the number of terms seem to decrease compared with level = 10. Why does this decrease? ...
written 17 months ago by b.nota330
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What does "level" argument mean in groupGO function (cluster profiler)?
... I want to use the groupGO function from cluster profiler, but do not exactly understand the level argument. The help page (hence ?groupGO) says: "Specific GO level." When I play around with it (giving it different numbers), I still don't seem to understand what and how this argument works. > gg ...
go clusterprofiler groupgo written 17 months ago by b.nota330 • updated 17 months ago by James W. MacDonald51k
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Comment: C: Compare groups of different RNAseq sets
... This sounds like a good solution, many thanks. I am going to give that a try! ...
written 17 months ago by b.nota330
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Comment: C: Compare groups of different RNAseq sets
... Thanks, I understand that. Just to be clear the experiments were both independent, with good design. But an additional question arose how a group in experiment 1 is compared to another group in a previous experiment. I mean what is the use of GEO data in this case? ...
written 17 months ago by b.nota330
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Compare groups of different RNAseq sets
... I would like to compare two groups (cell populations), from two different RNAseq experiments (sets). However, there are no overlapping groups in both experiments available, so an analysis in limma with batch effect (block design) is not possible. Let's say I have populations a, b, and c in experimen ...
limma batch effect written 17 months ago by b.nota330 • updated 17 months ago by Gordon Smyth38k
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Comment: C: Limma model for paired and pool together
... The pool is made of 3 other donors, so this will work for me! Thanks both. ...
written 17 months ago by b.nota330
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Limma model for paired and pool together
... I would like to use limma (voom or trend) for my RNAseq analysis, and I am wondering how to correctly model my data. I have 2 different cells (hi and lo) from 2 donors, so I want to use a paired design. However, there is also a pool of more donors (hi and lo). How can I include this correctly in my ...
rnaseq limma design written 17 months ago by b.nota330 • updated 17 months ago by Ryan C. Thompson7.4k

Latest awards to b.nota

Popular Question 9 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Popular Question 9 months ago, created a question with more than 1,000 views. For Limma voom or trend?
Popular Question 9 months ago, created a question with more than 1,000 views. For Postdoc bioinformatics in proteomics
Popular Question 16 months ago, created a question with more than 1,000 views. For How to get duplicate IDs numbered?
Popular Question 16 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Scholar 2.6 years ago, created an answer that has been accepted. For A: warning in R
Centurion 2.6 years ago, created 100 posts.
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Scholar 3.4 years ago, created an answer that has been accepted. For A: warning in R
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