User: Lluís R.
Lluís R. • 640
- Reputation:
- 640
- Status:
- Trusted
- Location:
- Spain, Barcelona
- Website:
- http://b101nfo.blogspo...
- Twitter:
- Lluis_Rev
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 hours ago
- Joined:
- 4 years, 3 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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... 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 12 days ago by
Lluís R. • 640
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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 13 days ago by
Lluís R. • 640
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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 17 days ago by
Lluís R. • 640
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... I hope that while finding the solution to this problem you also learned how to track down your bugs and solve them. Good luck! ...
written 9 weeks ago by
Lluís R. • 640
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... And the rownames of the count matrix you are using are the same symbol ids? ...
written 9 weeks ago by
Lluís R. • 640
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... And which type of list is it: one with genes: pathways or pathways genes? Load it as a GeneSetCollection and post here the output of printing it. I think that there are some gene sets with empty genes, or could be that the genes are not mapped to your matrix of probes/genes per sample ...
written 9 weeks ago by
Lluís R. • 640
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... No, `gsva` doesn't have any filtering parameter, the problem is with the `[1:186]` part ...
written 9 weeks ago by
Lluís R. • 640
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... Ok, are you sure you are using 186 Gene sets?? It seems like it is subseting by genes and not gene sets (subseting by number in a GeneSetCollection produces this, while subseting by name subsets by GeneSet name) or something alike. Where does the loadGSC function come from? Which class is the GSC.C2 ...
written 9 weeks ago by
Lluís R. • 640
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... If you aren't applying any filter by pathway size it might be a bug. Post it in support.bioconductor.org or https://github.com/rcastelo/GSVA/issues ...
written 9 weeks ago by
Lluís R. • 640
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... How many samples do you have on the original microarray data? If you had 6 samples then the expected output is 186(pathways provided)x6(samples) ...
written 9 weeks ago by
Lluís R. • 640
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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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