User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.3k
Reputation:
2,320
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Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
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Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
11 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 • 293 results • page 1 of 30 • next >
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Comment: C: GSVA on RNAseq data
... We used conditional quantile normalization with the [cqn][1] package because, back then, it seemed to us the most flexible and advanced normalization method for RNA-seq data, but we did not intend to make an specific advice to the users in this respect. Whether you need to adjust for GC and/or lengt ...
written 6 weeks ago by Robert Castelo2.3k
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Answer: A: GSVA on RNAseq data
... Hi Anja, the GSVA documentation does not make any recommendation as to what gene expression unit you should be using. It just tries to address the question about what should be the value for the argument 'kcdf'. More concretely, the help page says: > By default, ‘kcdf="Gaussian"’ which is suita ...
written 6 weeks ago by Robert Castelo2.3k
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Answer: A: GSVA lots of positive values, is this expected behavior?
... Hi, I would definitely remove lowly-expressed genes prior to running GSVA, just as you would do with differential expression. The fact that a gene set has consistently positive scores across samples means to me that its constituent genes are highly ranked in expression values across samples. chee ...
written 6 weeks ago by Robert Castelo2.3k
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Comment: C: Differential expression on GSVA scores using LIMMA
... Yes, note that while the magnitude of change may be tricky to interpret, the p-value has a very precise interpretation because rejecting the null hypothesis will allow you to say something about the association between the gene set and the explanatory variable for which the null hypothesis of its co ...
written 7 weeks ago by Robert Castelo2.3k
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Answer: A: Differential expression on GSVA scores using LIMMA
... hi, Negative values are not problematic with limma, in the same way that they are not when they derive from log CPM units in RNA-seq and you use the limma-trend pipeline, or with some microarray platforms (see this [post][1] about it). Regarding the interpretation of the GSVA units of expression, ...
written 7 weeks ago by Robert Castelo2.3k
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Answer: A: Are singscore scores comparable between gene sets?
... Hi, I can't comment on singscore, but the "gsva" default method implemented in the [GSVA][1] package, tries to make scores comparable across gene sets by first bringing gene expression profiles to a common scale, before summarizing the expression at gene set level. You can learn about the full meth ...
written 10 weeks ago by Robert Castelo2.3k
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Answer: A: Hill shape p-value histogram after differential miRNA expression analysis with D
... hi, i'd say that such a right-skewed distribution is often a product of some confounding factor that is not being adjusted. You can find a discussion on this in this old [thread][1] from the former Bioconductor mailing list. there has been also a more recent discussion about hill-shaped histograms ...
written 3 months ago by Robert Castelo2.3k
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Comment: C: Efficient counting of nucleotide changes in short-reads
... hi Michael, thanks for hint. i've been thinking looking at the documentation and examples on pileup() and thinking about it and i can't see how to use it because pileup() tallies nucleotides along the reference sequence, e.g.: seqnames pos strand nucleotide count 1 chr14 19069583 + ...
written 5 months ago by Robert Castelo2.3k
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Efficient counting of nucleotide changes in short-reads
... Dear BioC experts, I'm trying to do an efficient counting of all possible nucleotide changes between aligned nucleotides from short-read sequencing and corresponding reference nucleotides, i.e. how many A>C, A>G, A>T, C>A, C>G, C>T, etc. I have crafted a first approach using the B ...
biostrings genomicalignments written 5 months ago by Robert Castelo2.3k • updated 5 months ago by Michael Lawrence11k
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Comment: C: GSVA: enrichment score bounds and enrichment score transformations
... Whether results are reliable depends on many factors, probably most of them not related to GSVA. The recommendation about sample size refers to a minimum sample size on the total number of samples in the data set, because indeed, density estimation is performed across all samples regardless of sampl ...
written 5 months ago by Robert Castelo2.3k

Latest awards to Robert Castelo

Popular Question 6 months ago, created a question with more than 1,000 views. For Fisher-Yates algorithm for DNA shuffling ?
Popular Question 6 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Popular Question 6 months ago, created a question with more than 1,000 views. For problems installing VariantFiltering package
Popular Question 7 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Popular Question 8 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Scholar 12 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Teacher 23 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?
Scholar 23 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 23 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 23 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 2.0 years 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 2.0 years ago, voted at least 25 times.
Scholar 2.0 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
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?
Scholar 2.1 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 2.3 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 2.3 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 3.1 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 3.5 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist

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