User: Lluís R.
Lluís R. • 690
- Reputation:
- 690
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- Trusted
- Location:
- Spain, Barcelona
- Website:
- http://b101nfo.blogspo...
- Twitter:
- Lluis_Rev
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- Google Scholar Page
- Last seen:
- 1 day, 13 hours ago
- Joined:
- 4 years, 5 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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... If you are going right or not might be better addressed by your supervisor. But it seems reasonable to me ...
written 5 days ago by
Lluís R. • 690
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... The way that it is described in the tutorials of WGCNA, yes tumor 1 otherwise 0, but you could also have another variable that is stage, and that would be 0 no tumor, 1 small, 2 bigger, 3 metastasis or whatever. ...
written 9 days ago by
Lluís R. • 690
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... Well I don't know anything from this paper beyond what it is described, but looking for the Figure 4 a. it seems like they made the correlation between the condition and the eigengene. If it is accurate or not is another thing... You can do as them, but note that they have more than 4 samples for ea ...
written 10 days ago by
Lluís R. • 690
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... Your conditions seems like blocking factor. In the WGCNA it is recommended to make the correlation between the eigenvalue of the module with the phenotype variables. I would recommend however to do the correlation between the eigenvalue of the module with the eigenvalue of your condition.
However, ...
written 10 days ago by
Lluís R. • 690
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... Each time you run tSNE you'll get different results. I think you should be able to see this if you do another plot with Seurat and Monocle, you should see that it would change (unless they keep the same seed and random numbers). Also are you sure it is the same data? The first one is painted with tw ...
written 4 weeks ago by
Lluís R. • 690
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... You could then use DiffCoExp or DiffCoEx (not the same tools) that depend on WGCNA.
No, I was referring to the 2.b.5 section. ...
written 4 weeks ago by
Lluís R. • 690
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... How do you define the differentially connected genes? Genes that apear in the preserved consensus modules in both datasets? Or genes that change their connectivity and direction in each dataset?.
You can merge the clusters (now I don't remember in which tutorial is this explained, but there is one ...
written 5 weeks ago by
Lluís R. • 690
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... I haven't work with LC-MS data or tools so I can't recommend a package for this kind of data, but that one you linked seems a good one. Search the literature and papers that cite it to see if it fits your purpose (after you have read the methodology of the tool).
However it is different to test di ...
written 10 weeks ago by
Lluís R. • 690
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... In some context it seems that it should be enough to find some pattern that is common between conditions. If you want to find soft relationships between genes you need to have highly similar samples and that depends on the effect size of the changes of each condition, but with so many different cond ...
written 10 weeks ago by
Lluís R. • 690
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... You seem to have very low number of samples per conditions which makes this type of analysis unsuitable for you (if there are high differences by condition), It is recommended to use at least 20 samples for analysis which would mean mixing different conditions, thus making the groups of genes correl ...
written 11 weeks ago by
Lluís R. • 690
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For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
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For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
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