User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.2k
Reputation:
2,160
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Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
Scholar ID:
Google Scholar Page
Last seen:
1 week, 3 days ago
Joined:
11 years 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 • 276 results • page 1 of 28 • next >
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... the code and results above are based on the example of the help page of 'equalizeLibSizes()' from the edgeR package. If you read carefully that example you will see that (1) count values are sampled randomly from two different Poisson distributions, and therefore two different runs will give slightl ...
written 4 weeks ago by Robert Castelo2.2k
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Comment: C: Annotating Expression Set for GSVA w/ Brainarray Human Gene 1.1 ST Array CDF
... hi, this is not a GSVA-specific issue. The filtering of genes one does for GSVA is the same you would do for a differential expression analysis. The problem you show has to do the particular microarray chip to which the data you are analyzing belongs to and how to analyze it using the oligo package. ...
written 5 weeks ago by Robert Castelo2.2k
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... I think that for a gene-set level analysis you'll be fine with TMM-normalization and logCPM units per gene, which should be used with the Gaussian kernel. On the other hand, in a two recent publications (see Soneson et al., 2015, and Yi et al., 2018) it has been argued that calculating transcript-le ...
written 5 weeks ago by Robert Castelo2.2k
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... In one hand, Poisson kernels are only suitable for integer values, on the other hand, the GSVA algorithm assumes that the distributions of expression values across samples are comparable and thus that the input data are normalized. The help page of the  sample RNA-seq data used in the vignette of GS ...
written 5 weeks ago by Robert Castelo2.2k
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Comment: C: Problem using GOTERM[["x"]] from GO.db
... Excellent suggestion, thanks! ...
written 8 weeks ago by Robert Castelo2.2k
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Comment: C: Problem using GOTERM[["x"]] from GO.db
... I guess I'm missing something important here, but if AnnotationDbi would depend on a specific version of RSQLite, I thought (or rather I wished!) that R would not let updating RSQLite. Presumably, looking up reverse dependencies with specific versions is time consuming. So, in the end, containerizat ...
written 8 weeks ago by Robert Castelo2.2k
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Comment: C: Problem using GOTERM[["x"]] from GO.db
... I see, thanks for the further info about RSQLite, it's certainly bad luck that this didn't happen just a few weeks before, on time to fix both releases 3.6 and 3.7. I did not want to say that updating packages is difficult, but that either updating R or downgrading packages, may be difficult, surely ...
written 8 weeks ago by Robert Castelo2.2k
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Comment: C: Problem using GOTERM[["x"]] from GO.db
... Martin, AnnotationDbi is a package very upstream in the Bioconductor infrastructure, you need to scroll down quite a bit through its landing  web page to see all packages that either depend, import or suggest it. So, such an error essentially breaks the functionality of a large part of BioC packages ...
written 8 weeks ago by Robert Castelo2.2k
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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 12 weeks ago by Robert Castelo2.2k
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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 3 months ago by Robert Castelo2.2k

Latest awards to Robert Castelo

Scholar 12 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?
Scholar 12 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 12 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?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 13 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 14 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 14 months ago, voted at least 25 times.
Scholar 14 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Scholar 14 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 17 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 17 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 2.2 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
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?
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
Scholar 2.7 years ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 2.7 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 3.2 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 3.2 years ago, created an answer that has been accepted. For A: phastCons scores for GRCh38
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.9 years ago, created 100 posts.

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