User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.0k
Reputation:
1,980
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Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
Scholar ID:
Google Scholar Page
Last seen:
14 hours ago
Joined:
9 years, 12 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 • 234 results • page 1 of 24 • next >
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Comment: C: RNAseq with technical replicates: Does it sound right?
... Before adding the raw counts across lanes, I would also do an MDS plot of all the 108 files labeled by an index of the biological sample identity and colored by lane, to assess the similarity between technical replicates from the same biological sample, they should overlap on the same spot. ...
written 14 hours ago by Robert Castelo2.0k
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Answer: A: GSVA: questions about the bootstrap p-value
... hi, sorry for the delay in getting back to you. I'm a contributor to GSVA and not the maintainer of the package who added this feature but I'll try to answer. Indeed, bootstrapping was something added after the publication, which is the main reason why is not well described. Let me warn you that th ...
written 7 days ago by Robert Castelo2.0k
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Comment: C: mm10 phastCons data for use with ATACseqQC
... hi, thanks for your patience, i've edited my answer above, a 'GScores' object has now become available for phastCons60way.UCSC.mm10. cheers, robert. ...
written 26 days ago by Robert Castelo2.0k
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Answer: A: mm10 phastCons data for use with ATACseqQC
... hi, i'm the maintainer of phastCons100way.UCSC.hg19, this package reduces the memory requirements by rounding the phastCons scores to 1-decimal digit, i'm in the process of generating other types of GScores objects, including for instance phyloP scores with a different quantization adapted to this k ...
written 4 weeks ago by Robert Castelo2.0k
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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 5 weeks ago by Robert Castelo2.0k
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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 5 weeks ago by Robert Castelo2.0k
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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 5 weeks ago by Robert Castelo2.0k
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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 6 weeks ago by Robert Castelo2.0k
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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 7 weeks ago by Robert Castelo2.0k
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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 7 weeks ago by Robert Castelo2.0k

Latest awards to Robert Castelo

Scholar 15 days 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 5 weeks 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 5 weeks ago, voted at least 25 times.
Scholar 7 weeks ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 7 weeks ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 5 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 5 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
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 18 months ago, created a post with more than 5 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: Network generation from adjacency matrix of zeroes and ones
Scholar 19 months ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 19 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.2 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.2 years ago, created an answer that has been accepted. For A: phastCons scores for GRCh38
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Autobiographer 2.8 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 2.9 years ago, created 100 posts.

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