User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.1k
Reputation:
2,110
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Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
Scholar ID:
Google Scholar Page
Last seen:
2 days, 19 hours ago
Joined:
10 years, 9 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 • 268 results • page 1 of 27 • next >
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Answer: A: Input genes for GSVA
... hi, The question on having "more appropriate background distributions" has more to do with having sufficient sample size for the first step in which GSVA evaluates whether a gene is highly or lowly expressed in a sample. But I understand your question is rather about the input number of genes. As d ...
written 2 days ago by Robert Castelo2.1k
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Answer: A: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... Hi, regarding ssGSEA, I implemented the method in the GSVA package but I did not developed it; see the original publication by Barbie et al. (2009) for the methodological details. My understanding is that it was designed for microarray data (see documentation of its official implementation in GeneP ...
written 21 days ago by Robert Castelo2.1k
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Comment: C: Does GSVA enrichment score comes negative?
... Hi Prat, if you are using GSVA scores for inferential purposes such as selecting gene sets that are differentially expressed, then i'd recommend to start with the whole set of genes, discard those that are lowly expressed and calculate GSVA scores over the collection of gene sets of your interest. ...
written 29 days ago by Robert Castelo2.1k
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Comment: C: Does GSVA enrichment score comes negative?
... Hi Prat, please read carefully the Bioconductor Posting Guide, which contains guidelines on what are the best practices in using this support site. These best practices are there for the benefit of everyone, including your own. In particular, if you look at the guidelines for "Composing", the first ...
written 4 weeks ago by Robert Castelo2.1k
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Comment: C: The selection of bandwidth of GSVA
... We were happy with how the whole approach was working in the different applications shown in the paper. This, however, does not mean that the choice we made is the best one for every possible application and there might be room for improvement by making a more careful choice of bandwidth. If users f ...
written 5 weeks ago by Robert Castelo2.1k
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Answer: A: The selection of bandwidth of GSVA
... hi, we chose this fixed setting because from our experience it worked well in practice. robert. ...
written 6 weeks ago by Robert Castelo2.1k
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Answer: A: GSVA for single sample
... hi, you have a typo in your code, the '==' operator is for comparison, not for assignment. please replace method == "ssgsea" by method = "ssgsea" and it will work. cheers, robert. ...
written 10 weeks ago by Robert Castelo2.1k
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Answer: A: Run tweeDEseq on Flux-capacitor RPKM values
... Dear Fazulur, 1. No, you can not use RPKM values as input to the tweeDEseq package. This package implements a statistical model based on Poisson-Tweedie distributions for count values and RPKM values are not count values. 2. No, for the same reason I give on your first question. As a side note, w ...
written 10 weeks ago by Robert Castelo2.1k
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Answer: A: Error thrown by GSEABase::getBroadSets function: Error: 'getBroadSets' failed to
... hi, I've just tried it out with the current release version of R 3.4.2 and the GSEABase package (1.40.1) and it works fine. You need to update to the  current R release version 3.4.2 and current release of Bioconductor; see http://bioconductor.org/install. library(GSEABase) MSigDB <- getBroadS ...
written 4 months ago by Robert Castelo2.1k
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Comment: C: [gwascat] Updated GWAS catalog from file
... I see three options: write a wrapper function for your students, parse the gwascat file yourself and provide your students directly with the 'GRanges' object, or contact the package maintainer to request further functionality. ...
written 4 months ago by Robert Castelo2.1k

Latest awards to Robert Castelo

Scholar 10 months ago, created an answer that has been accepted. For A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Teacher 11 months 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 11 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 11 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 14 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 14 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 24 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
Scholar 2.4 years ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 2.4 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 3.0 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 3.0 years ago, created an answer that has been accepted. For A: phastCons scores for GRCh38
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.7 years ago, created 100 posts.

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