User: b.nota

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b.nota290
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Posts by b.nota

<prev • 135 results • page 1 of 14 • next >
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Comment: C: limma roast results not in accordance with barcodeplot
... Thanks (again) for your help, it's really appreciated. It was indeed the index that was not correct. I used for roast only the ensemble gene names of interest (which worked, but was not correct). With barcodeplot this index gave an error, which is why I used the index vector like in your example ind ...
written 5 weeks ago by b.nota290
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limma roast results not in accordance with barcodeplot
... I am trying to use limma roast, as advised in a previous post post. However, I have doubts about if it is correct what I am doing, since the barcodeplot gives a different picture of my results. I have an RNA-seq experiment analyzed with limma trend, and want to see if a signature of 48 genes (from a ...
limma roast written 5 weeks ago by b.nota290
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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 6 weeks ago by b.nota290
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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 6 weeks ago by b.nota290
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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 7 weeks ago by b.nota290
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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 7 weeks ago by b.nota290
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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 7 weeks ago by b.nota290 • updated 7 weeks ago by James W. MacDonald46k
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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 7 weeks ago by b.nota290
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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 7 weeks ago by b.nota290
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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 7 weeks ago by b.nota290 • updated 7 weeks ago by Gordon Smyth33k

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