User: Lluís R.
Lluís R. • 880
- Reputation:
- 880
- Status:
- Trusted
- Location:
- Spain, Barcelona
- Website:
- http://b101nfo.blogspo...
- Twitter:
- Lluis_Rev
- Scholar ID:
- Google Scholar Page
- Last seen:
- an hour ago
- Joined:
- 5 years, 10 months ago
- Email:
- l************@gmail.com
I am interested nowadays in microarrays, RNA-Seq and genome annotation, GO and pathways. But my goal are to maximize the useful information of each existing experiment. Now I am committing with Bioconductor, you can follow some of my thought in my blog, or in twitter.
Posts by Lluís R.
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... You keep using the word network but you don't specify in which format do you have this network. How are the edges and nodes of this network stored? Or these custom network is just a list of co-expressed or a selection of genes? ...
written 2 days ago by
Lluís R. • 880
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... You are commenting that you have a list of genes that are networks. How do you define those networks ? And what type of enrichment are you looking for? ...
written 5 days ago by
Lluís R. • 880
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... I have some data that I model with 4 factors, each one have two levels. However, I need to compare some samples based on a fifth factor that is not included on the model:
Here I provide an example design matrix:
groups <- paste(c("f1A", "f1B", "f1A", "f1A", "f1B", "f1A"),
...
written 8 days ago by
Lluís R. • 880
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Comment:
C: High fold change values
... I don't think it is. You can find the boxplot [here](https://i.ibb.co/5rmrFhc/log-CPM.png), also here [after voom](https://i.ibb.co/QPftzCy/voom-boxplot.png) normalization ...
written 12 days ago by
Lluís R. • 880
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Comment:
C: High fold change values
... I filtered using `edgeR::filterByExpr`, that is min.count = 10 and min.total.count = 15. But I haven't looked at cpm, I'll look at it. When I mention the 75% of DEG is looking only to the FDR < 0.05. ...
written 13 days ago by
Lluís R. • 880
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... I am studying some RNA-seq data with `edgeR` and `limma`. The data was obtained from 59 samples using Illumina HiSeq 2500 and analyzing following the workflow [RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR ][1].
The data is quite complex with 4 different factors interacting betwee ...
written 13 days ago by
Lluís R. • 880
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... How do you define enrichment of clusters of grouped GO IDs? The higher they are similar between them the earlier your clusters will merge ...
written 14 days ago by
Lluís R. • 880
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... You can use GOSemSim to compare list of GO. It compares them based on semantic similarity of GO terms. ...
written 14 days ago by
Lluís R. • 880
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67k
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Comment:
C: How To Merge Two Fastq.Gz Files?
... Probably the compression found more patterns when more data was added, thus it could reduce more information. ...
written 10 weeks ago by
Lluís R. • 880
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... As this seems to be popular since then there is a [package][1] BiocPkgTools, currently only in github to download and analyse the data
[1]: https://seandavi.github.io/BiocPkgTools/articles/BiocPkgTools.html#download-statistics ...
written 7 months ago by
Lluís R. • 880
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For Google Summer Of Code 2014 Gsoc 2014
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11 months ago,
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For A: Difference between GO.db, biomaRt, and org.Hs.eg.db in GO annotations
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For A: Difference between GO.db, biomaRt, and org.Hs.eg.db in GO annotations
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15 months ago,
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For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
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