User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.3k
Reputation:
2,260
Status:
Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
11 years, 6 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 • 286 results • page 1 of 29 • next >
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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 weeks 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 weeks ago by Robert Castelo2.3k • updated 5 weeks ago by Michael Lawrence10k
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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 7 weeks ago by Robert Castelo2.3k
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Answer: A: GSVA: enrichment score bounds and enrichment score transformations
... Hi Sarah, GSVA enrichment scores, as defined by Eq. (5) in the GSVA article, are bound between -1 and 1 because they arise from the difference between two empirical cumulative distribution functions (ECDFs), which themselves, as such, are bound between 0 and 1. you mention that your GSVA scores ar ...
written 11 weeks ago by Robert Castelo2.3k
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Answer: A: Differential Expression of GSVA Enrichment Scores - pre-processing with voomWith
... Hi, others may give you more specific advice about using voomWithQualityWeights but if you look at the documentation you'll see that this function allows you to use the power of voom with the power of sample-specific weights. The latter are specially useful when samples have very different qualitie ...
written 3 months ago by Robert Castelo2.3k
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Answer: A: GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
... Hi, thanks for bringing this up. It escaped to our attention since only the *_up signatures (gene sets) are used in the vignette that illustrates their use, and this coincidence is happening with a *_dn gene set. These signatures were derived from the publication by Cahoy et al. (2008) but I cannot ...
written 4 months ago by Robert Castelo2.3k
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Answer: A: GSVA & Limma for DE of Gene Sets using NanoString Data
... hi, regarding the GSVA transformation, the parameters you have used seem fine to me. The rest of the question seems to be more related to general experimental design. I would try though to have both analysis, at feature level and gene-set level and try to have a sense whether you are using the appro ...
written 4 months ago by Robert Castelo2.3k
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Comment: C: Meaning of zero for ssGESA value calculated by GSVA package
... Yes. The meaning of GSVA negative scores has been in fact already asked in this support site in this thread. cheers, robert. ...
written 6 months ago by Robert Castelo2.3k
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Answer: A: Meaning of zero for ssGESA value calculated by GSVA package
... Hi Shixiang, We did not develop the ssGSEA method, we just implemented it in the GSVA package. The methodological descriptions in the online manual and the vignette of GSVA refer to the GSVA (deafult) method. The ssGSEA method was introduced by Barbie et al. (2009), where you can find its descripti ...
written 6 months ago by Robert Castelo2.3k
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Answer: A: GSVA with NanoString nCounter Data - Pre-Processing
... hi, i have no experience with NanoString nCounter data so i cannot give you an specific advice in using GSVA with this technology. GSVA does not perform any normalization of the data and it is the responsibility of the user to provide data normalized to the 'gsva()' function. Normalizing data essen ...
written 6 months ago by Robert Castelo2.3k

Latest awards to Robert Castelo

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Fisher-Yates algorithm for DNA shuffling ?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Popular Question 9 weeks ago, created a question with more than 1,000 views. For problems installing VariantFiltering package
Popular Question 3 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Popular Question 4 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Scholar 8 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Teacher 19 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 19 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 19 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
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: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Teacher 20 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 20 months ago, voted at least 25 times.
Scholar 20 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 21 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
Scholar 24 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 2.7 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
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?
Scholar 3.2 years ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 3.2 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist

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