User: Leonardo Collado Torres

Reputation:
590
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Trusted
Location:
United States
Website:
http://lcolladotor.git...
Twitter:
fellgernon
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Last seen:
1 month, 3 weeks ago
Joined:
8 years, 4 months ago
Email:
l*******@jhu.edu

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 • 165 results • page 1 of 17 • next >
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Comment: C: derfinder: how to merge regions and counts from individual chromosomes
... I added this as an example in regionMatrix() to derfinder version 1.13.1. Details: https://github.com/lcolladotor/derfinder/commit/cb7f8bdb9d99aae0a86758aa3e5bde00712a14d6 ...
written 7 weeks ago by Leonardo Collado Torres590
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Answer: A: derfinder: how to merge regions and counts from individual chromosomes
... Hi, You can combine the different pieces of regionMat (the one that is a list with one element per chromosome) manually as shown in the code below: library('derfinder') ## Modified code from ?regionMatrix ## Create some toy data library('IRanges') x <- Rle(round(runif(1e4, max=10))) y <- ...
written 7 weeks ago by Leonardo Collado Torres590
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Comment: C: Time-course group difference analysis with repeated individuals using limma-voom
... Thanks Aaron! Best, Leo ...
written 7 weeks ago by Leonardo Collado Torres590
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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 8 weeks ago by Leonardo Collado Torres590
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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 8 weeks ago by Leonardo Collado Torres590 • updated 8 weeks ago by Aaron Lun18k
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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 8 weeks ago by Leonardo Collado Torres590
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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 weeks ago by Leonardo Collado Torres590
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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 3 months ago by Leonardo Collado Torres590
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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 3 months ago by Leonardo Collado Torres590
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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 ...

Latest awards to Leonardo Collado Torres

Scholar 7 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Supporter 9 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 21 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Centurion 21 months ago, created 100 posts.
Scholar 2.6 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 3.2 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Scholar 3.3 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.

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