User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.2k
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2,240
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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 week, 1 day ago
Joined:
11 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 • 283 results • page 1 of 29 • next >
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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 8 days ago by Robert Castelo2.2k
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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 28 days ago by Robert Castelo2.2k
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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 8 weeks ago by Robert Castelo2.2k
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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 8 weeks ago by Robert Castelo2.2k
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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 3 months ago by Robert Castelo2.2k
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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 3 months ago by Robert Castelo2.2k
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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 3 months ago by Robert Castelo2.2k
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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 5 months 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 months 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 months ago by Robert Castelo2.2k

Latest awards to Robert Castelo

Popular Question 8 weeks ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Scholar 6 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
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?
Scholar 16 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 16 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 16 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 17 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 18 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 18 months ago, voted at least 25 times.
Scholar 18 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 18 months ago, created an answer with at least 3 up-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: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 21 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
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 2.6 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
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?
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 2.9 years ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
Scholar 3.0 years ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 3.0 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 3.6 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 3.6 years ago, created an answer that has been accepted. For A: phastCons scores for GRCh38
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions

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