User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.0k
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Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
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Google Scholar Page
Last seen:
2 weeks, 4 days ago
Joined:
10 years, 3 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 • 249 results • page 1 of 25 • next >
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Comment: C: GSVA package scores are opposite on mac and windows
... Thanks Martin, then @Jason one possible way forward for you would be to install the former release version of R 3.4.1 and install the BioC packages on that version. ...
written 18 days ago by Robert Castelo2.0k • updated 18 days ago by Martin Morgan ♦♦ 20k
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Comment: C: GSVA package scores are opposite on mac and windows
... hi, the only difference i see is that you use R 3.4.2 and i was using 3.4.0. i've updated R in my macOS sierra to 3.4.2 and run again the code. unfortunately i cannot reproduce the problem, i get exactly the same numbers as with linux. i don't know what can i do about it if i cannot reproduce the er ...
written 18 days ago by Robert Castelo2.0k
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Comment: C: GSVA package scores are opposite on mac and windows
... Hi Jason, thanks for posting the session information. According to it, you are using the very latest GSVA development version 1.25.6. However, under that version, the code posted above would not work because in the current devel version we have deprecated the way in which scores calculated by the de ...
written 18 days ago by Robert Castelo2.0k
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Comment: C: GSVA package scores are opposite on mac and windows
... hi again, sorry i didn't realize you were talking about the development version. I've edited my answer to address the question with respect to the development version. In any case, it is always recommended to use the release version. ...
written 18 days ago by Robert Castelo2.0k
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Comment: C: GSVA package scores are opposite on mac and windows
... hi, the function 'gsva()' uses by default the GSVA method introduced in the GSVA paper, but it does provide the user the possibility to calculate right-singular vectors as summaries of pathway expression by setting the argument 'method="plage". I've tried that and indeed the resulting values are inv ...
written 18 days ago by Robert Castelo2.0k
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Answer: A: GSVA package scores are opposite on mac and windows
... Dear Jason, thanks for your message. I don't have access to a windows machine but I do have an apple laptop with macOS Sierra (10.12.6) and i cannot reproduce the problem in the release nor in the development version. i get exactly the same numbers in macOS and in linux. I'm providing here below my ...
written 18 days ago by Robert Castelo2.0k
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Comment: C: Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(
... thanks! does the use of the NB mean for filtering lowly-expressed genes still applies if, instead of edgeR, i use the limma-voom pipeline for differential expression? ...
written 5 weeks ago by Robert Castelo2.0k
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Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
... hi, the documentation of the aveLogCPM() function from edgeR says that this function is similar to: log2(rowMeans(cpm(y, ...))) because CPM values may be more disperse than logCPM values and the arithmetic mean is sensitive to outliers, would not make more sense that aveLogCPM() resembles rowMea ...
rnaseq limma edger independent filtering written 5 weeks ago by Robert Castelo2.0k
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Comment: C: Bioconductor packages now each have a DOI.
... Great, I think it would be useful that the DOI is shown in the package landing page, ideally by fetching it from the package DESCRIPTION file, if such a field would be allowed. ...
written 6 weeks ago by Robert Castelo2.0k
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Answer: A: Set rnaseq locial flag during GSVA
... Hi, sorry for the very long delay in answering your question. I see that the documentation may be confusing with respect to the necessity or not of the logarithmic scale but the crucial point made by the documentation is that rnaseq=TRUE "is only suitable when the input gene expression matrix is for ...
written 6 weeks ago by Robert Castelo2.0k

Latest awards to Robert Castelo

Scholar 4 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 5 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 5 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 5 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 9 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 9 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 18 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 22 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 22 months ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
Scholar 23 months ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
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: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.5 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.5 years ago, created an answer that has been accepted. For A: phastCons scores for GRCh38
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Autobiographer 3.1 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.2 years ago, created 100 posts.

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