User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.3k
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2,330
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Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
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Google Scholar Page
Last seen:
1 month ago
Joined:
12 years, 4 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 • 297 results • page 1 of 30 • next >
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Answer: A: How to build and map to a "pre-mRNA" reference transcriptome for single nucleus
... I recently had to deal with intronic reads from a bulk total RNA sequencing experiment (see Fig. 1a from this [preprint](https://www.medrxiv.org/content/10.1101/19000109v2)) and derived an intronic annotation for that purpose using Bioconductor. Our aim was to count strictly intronic reads. If this ...
written 5 weeks ago by Robert Castelo2.3k
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Comment: C: SVA for repeated measures design
... If `SUBJECT.ID` is a random factor, then you should not put it into the design matrix and use `duplicateCorrelation()` and the arguments `correlation` and `block` in the call to `lmFit()`; see section on Multi-level experiments from the limma User's Guide. If you don't need surrogate variables, then ...
written 6 weeks ago by Robert Castelo2.3k
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Answer: A: SVA for repeated measures design
... Hi, I would say the answer is **to include** SUBJECT.ID in the null model because, as argued by Jeff Leek, author of SVA, in this [thread](https://support.bioconductor.org/p/54719) about a similar design case, SUBJECT.ID will be used in the ultimate linear model you intend to fit to test for the ef ...
written 6 weeks ago by Robert Castelo2.3k
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Answer: A: Collecting unmapped RNA-seq reads
... I don't know about subread-align but outside BioC, the [STAR](https://github.com/alexdobin/STAR) aligner offers the option --outReadsUnmapped Fastx that will dump the unmapped reads to FASTQ files. cheers, robert. ...
written 10 weeks ago by Robert Castelo2.3k
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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 7 months 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 7 months 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 7 months 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 months 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 months 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 8 months ago by Robert Castelo2.3k

Latest awards to Robert Castelo

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Differential expression on GSVA scores using LIMMA
Popular Question 11 months ago, created a question with more than 1,000 views. For GO term as "keytype" in GO.db
Popular Question 11 months ago, created a question with more than 1,000 views. For working with genome-wide phastCons scores
Scholar 11 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Popular Question 12 months ago, created a question with more than 1,000 views. For problems installing VariantFiltering package
Popular Question 12 months ago, created a question with more than 1,000 views. For Fisher-Yates algorithm for DNA shuffling ?
Popular Question 12 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Popular Question 13 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Popular Question 14 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Scholar 18 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
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: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Scholar 2.4 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 2.4 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?
Scholar 2.4 years 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 2.5 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 2.5 years ago, voted at least 25 times.
Scholar 2.5 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Scholar 2.5 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 2.8 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 3.6 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 3.9 years ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?

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