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 • 177 results • page 2 of 18 • next >
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Answer: A: Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?
... Since I don't know any other way of "closing" a question, I'll just say that I failed in this case to provide a reproducible example 3.3 years ago. See https://support.bioconductor.org/p/62026/#105654. ...
written 10 months ago by Leonardo Collado Torres610
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Comment: C: Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?
... Sorry, this was so long ago that I don't remember. I even forgot about this thread and as you can see, I never got around to providing a reproducible example. Guess I can use this thread as an example of what not to do in the Bioc support website.   My guess from using `qvalue` in other projects i ...
written 10 months ago by Leonardo Collado Torres610
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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 12 months ago by Leonardo Collado Torres610
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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 12 months ago by Leonardo Collado Torres610
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Comment: C: Time-course group difference analysis with repeated individuals using limma-voom
... Thanks Aaron! Best, Leo ...
written 12 months ago by Leonardo Collado Torres610
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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 12 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 12 months ago by Leonardo Collado Torres610 • updated 12 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 12 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 13 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 14 months ago by Leonardo Collado Torres610

Latest awards to Leonardo Collado Torres

Popular Question 6 weeks 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
Popular Question 6 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 6 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 17 months ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 17 months ago, created an answer that has been accepted. For A: Number of IRanges elements in TCGA HiSeqV2 dataset
Scholar 17 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 17 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 17 months ago, created an answer that has been accepted. For A: derfinder: analyzeChr() breaks on chromosomes > 22
Scholar 17 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Popular Question 17 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 17 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 18 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Supporter 20 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 2.6 years ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Centurion 2.6 years ago, created 100 posts.
Scholar 3.5 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 4.1 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 4.1 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Autobiographer 4.2 years ago, has more than 80 characters in the information field of the user's profile.

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