User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo1.9k
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1,950
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Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
Scholar ID:
Google Scholar Page
Last seen:
5 hours ago
Joined:
9 years, 10 months ago
Email:
r*************@upf.edu

Associate professor of Bioinformatics and Biostatistics at the Universitat Pompeu Fabra in Barcelona (Spain). PhD in Computer Science by the University of Utrecht, The Netherlands (2002).

I develop and maintain the R/BioC software packages qpgraph, GenomicScores and VariantFiltering and have contributed to the development of the GSVA and tweeDEseq software packages. I'm also contributing and maintaining the annotation packages phastCons100way.*, MafDb.* and fitCons.UCSC.hg19, and some AnnotationHub resources available from the GenomicScores package.

Posts by Robert Castelo

<prev • 230 results • page 1 of 23 • next >
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
... hi, i think that the large user base of moderated t-tests, and the large number of publications using them, lead to more scrutiny on how these methods work. So, i'd say that if moderated t-tests would be systematically behind irreproducible results in the scientific literature, their responsibility ...
written 17 hours ago by Robert Castelo1.9k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
... I have edited my original answer to add two more panels to the third figure, to show the raw p-values of the classical t-test and the moderated t-test, calculated on the subset of 6 samples, as function of the raw p-values of the classical t-test calculated on the whole set of available samples (71) ...
written 1 day ago by Robert Castelo1.9k
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Answer: A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
... hi, Just in case you find this useful, when I try to show my students the difference between a classical t-test and a moderated t-test that borrows information across genes, such as the one implemented in the limma package, without showing any formulas, I show them the following three sets of plots ...
written 3 days ago by Robert Castelo1.9k
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Comment: C: Does GSVA enrichment score comes negative?
... Hi Prat, please next time to use the 'ADD COMMENT' link, which i'm using right now, to make comments, remarks and/or follow up questions, such as your two last messages in this page, to keep the answer slots only for new answers. this helps structuring conversation about a particular topic. regard ...
written 14 days ago by Robert Castelo1.9k
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Answer: A: FUNCTIONAL ENRICHMENT ANALYSIS
... hi, It's unclear to me to what Bioconductor package are your referring to when you talk about the "genecodis3 tools" as a text-free search among the software packages does not give any hit. About the general question on how to select enriched GO terms, there are many options, just think for instan ...
written 14 days ago by Robert Castelo1.9k
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Answer: A: GSVA indifferent to 'abs.ranking'
... Dear Sina, thank you very much for your detailed bug report. Indeed, the calculation of GSVA scores with the non-default configuration where 'abs.ranking=TRUE' was doing the same calculations as if 'abs.ranking=FALSE', as long as the default 'kernel=TRUE' remained unchanged, otherwise ('kernel=FALS ...
written 15 days ago by Robert Castelo1.9k
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Answer: A: Crash GSVA 1.24.0 with bootstrapping
... hi, thanks for the report and the code reproducing the error. The background problem is that you are giving to the algorithm the whole data set. if you look closely to the output of the GSVA run without bootstrapping, you'll see a warning message saying that a number of genes had constant expressio ...
written 20 days ago by Robert Castelo1.9k
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Answer: A: How to convert graphNEL object into Adjacency Matrix?
... hi, the way you formulate the question is not completely clear to me but i guess you're asking how to coerce a 'graphNEL' object to an adjacency matrix. this can be done using as(g, "matrix") where 'g' would be the 'graphNEL' object, here's an example: library(graph) g <- graphNEL(nodes=LET ...
written 27 days ago by Robert Castelo1.9k
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Answer: A: qpgraph's qpPCC function giving different results than cor.test()
... hi, thanks for bringing this issue up. i'm afraid the documentation of the function qpPCC() is not accurate because it does behave differently to using cor.test() in the presence of missing values. more concretely, qpPCC() uses only complete observations across all variables in the input data. if y ...
written 3 months ago by Robert Castelo1.9k
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Comment: C: [GSVM] bootstrapping error
... Great! Please remember next time to add 'GSVA' as tag to the question to make it easier for me to spot it. ...
written 4 months ago by Robert Castelo1.9k

Latest awards to Robert Castelo

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Supporter 3 days ago, voted at least 25 times.
Scholar 14 days ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Scholar 20 days ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 3 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 3 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 13 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 17 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 17 months ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
Scholar 18 months ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 18 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.1 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.1 years ago, created an answer that has been accepted. For A: phastCons scores for GRCh38
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 2.8 years ago, created 100 posts.

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