User: Leonardo Collado Torres

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http://lcolladotor.git...
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Leonardo Collado Torres, Ph. D., Data Scientist
Lieber Institute for Brain Development
Clinical Sciences Division
855 N Wolfe St, Suite 300
Baltimore, MD 21205

Website: http://lcolladotor.github.io/about.html
Blog: http://lcolladotor.github.io/

 

Posts by Leonardo Collado Torres

<prev • 172 results • page 2 of 18 • next >
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Comment: C: Time-course group difference analysis with repeated individuals using limma-voom
... Hi, While I did figure out my main problem, I decided it would still be worth posting just as an example of how completing all the Bioconductor posting guide steps can help users find their own problem.  In my case, when I was writing the last part of my question, I realized that maybe I wasn't co ...
written 10 months ago by Leonardo Collado Torres610
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Time-course group difference analysis with repeated individuals using limma-voom
... Hi, From the limmaUsersGuide() section "9.7 Multi-level Experiments" I learned about using duplicateCorrelation() and passing that information to lmFit() to handle observations from the same individual (using block and correlation arguments). Similarly, from "9.6.2 Many time points" I learned about ...
limma written 10 months ago by Leonardo Collado Torres610 • updated 10 months ago by Aaron Lun21k
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Answer: A: derfinder mean Expressed Region cutoff
... Hi, Maybe the wording in the paper could have been clearer. Once you have a mean coverage vector (in reality a Rle object), we use a single global cutoff for finding the expressed regions. Just like in Figure 2A of the derfinder paper https://academic.oup.com/nar/article/45/2/e9/2953306.  For choo ...
written 10 months ago by Leonardo Collado Torres610
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Answer: A: Getting pheno tables from recount datasets without any NA values in characterist
... Hi Mustafa, Nearly 13k samples from the SRA ones don't have any characteristics or GEO accession numbers as shown with the code below. There's nothing we can really do about it. Sometimes updates in SRAdb include new GEO accession numbers. The issue with sample metadata being incomplete is a proble ...
written 10 months ago by Leonardo Collado Torres610
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Comment: C: NA values of count matrix in class DESeqDataSet
... Looks like the same as this question https://support.bioconductor.org/p/100791 ...
written 11 months ago by Leonardo Collado Torres610
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Comment: C: NA values of count matrix in class DESeqDataSet
... Hi, Please post code for reproducing the error and the R session information you have. Thanks. Also, why are you writing the colData() information to a text file and then reading it back into R? Are you editing the colData() information outside R? Best, Leonardo ...
written 11 months ago by Leonardo Collado Torres610
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Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
... Hi, The following code used to work in R 3.3 with Bioconductor 3.4. It now fails on a linux machine I have access to with both Bioc 3.5 and 3.6 but works in my OSX laptop with the same versions. library(bumphunter) library(TxDb.Hsapiens.UCSC.hg38.knownGene) gene <- annotateTranscripts(txdb = T ...
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Answer: A: Recount TCGA data
... Hi, The text files are missing the gene ids. I realize this is an inconvenience if you don't want to use R. This information is much more well organized in the RangedSummarizedExperiment objects (RSE) that you can download from https://jhubiostatistics.shinyapps.io/recount/ or via the recount Bioc ...
written 12 months ago by Leonardo Collado Torres610
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Comment: C: How to preserve the strand of coverage in derfinder::regionMatrix() ?
... https://bioconductor.org/packages/release/bioc/vignettes/derfinder/inst/doc/derfinder-users-guide.html#controlling-loading-from-bam-files ...
written 12 months ago by Leonardo Collado Torres610
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Answer: A: How to preserve the strand of coverage in derfinder::regionMatrix() ?
... Hi, If you have stranded RNA-seq data you have to process each strand separately. If you have BAM files, that means using the appropriate Rsamtools::scanBamFlag() information. If you have BigWig files for each strand, then that means importing the data for one strand at a time. You can then add the ...
written 12 months ago by Leonardo Collado Torres610

Latest awards to Leonardo Collado Torres

Popular Question 4 months ago, created a question with more than 1,000 views. For Getting a flat metadata table from the XML files in TCGA: is it feasible?
Popular Question 4 months ago, created a question with more than 1,000 views. For Trying to use the liftOver function from the rtracklayer package in R 2.14.0
Scholar 15 months ago, created an answer that has been accepted. For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Scholar 15 months ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 15 months ago, created an answer that has been accepted. For A: Issue creating a genomic state object in derfinder from an Ensembl GTF file
Scholar 15 months ago, created an answer that has been accepted. For A: Is it possible to read bigwig files with rtracklayer over https? Comes down to G
Scholar 15 months ago, created an answer that has been accepted. For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar 15 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Popular Question 15 months ago, created a question with more than 1,000 views. For Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Popular Question 15 months ago, created a question with more than 1,000 views. For Trying to use the liftOver function from the rtracklayer package in R 2.14.0
Scholar 15 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
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Scholar 18 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
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Scholar 3.3 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 3.9 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Scholar 3.9 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
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