User: Tiago Chedraoui Silva

Reputation:
240
Status:
Trusted
Location:
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
4 years, 1 month ago
Email:
t********@usp.br

Posts by Tiago Chedraoui Silva

<prev • 84 results • page 1 of 9 • next >
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Comment: C: Missing Clinical LIHC Data
... I need to check better your code to understand it. Unfortunately I don't have a lot of time now. But: 1) did you tried the indexed clinical data? This should be the clinical data with the follow up updated. index.clinical <- GDCquery_clinic("TCGA-LIHC") index.clinical[,c("days_to_last_follow_up ...
written 8 days ago by Tiago Chedraoui Silva240
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Comment: C: Matching TCGA Aliquot ID to UUID or Barcode
... It seems the UUID you have '56467ebd-af89-4413-84b5-1e00699a2744' is the file ID that contains multiple Barcodes (https://imgshare.io/image/vYlHe) ...
written 28 days ago by Tiago Chedraoui Silva240
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Comment: C: ELMER::createMAE() Error: $ operator is invalid for atomic vectors
... Thanks for the example, but it is working on my side that part of the code. It is accessing ENSEMBL database using biomart. There was a change recently in one of the fields name. Please, could you try updating TCGAbiolinks and ELMER and try again. You should have ELMER 2.9.3 now. BiocManager: ...
written 4 months ago by Tiago Chedraoui Silva240
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Answer: C: ELMER::createMAE() Error: $ operator is invalid for atomic vectors
... Please, can you update to the GitHub version with: BiocManager::install(c("tiagochst/ELMER.data","tiagochst/ELMER")) I believe that was solved recently, but the updates are not in Bioconductor yet. ...
written 4 months ago by Tiago Chedraoui Silva240
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Answer: A: Matching TCGA Aliquot ID to UUID or Barcode
... In TCGAbiolinks, when reading the copy number data we use the GDC API to map the aliquot id to barcode: https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1182-L1211 ...
written 4 months ago by Tiago Chedraoui Silva240
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Answer: A: TCGAbiolinks : Bisulfite-seq data : Legacy archive
... The correct code to access WGBS would be: query <- GDCquery(project = c("TCGA-COAD"), legacy = TRUE, data.category = "DNA methylation", data.type = "Methylation percentage", experimental.strategy = "Bisul ...
written 4 months ago by Tiago Chedraoui Silva240
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Answer: A: Missing clinical data at TCGAbiolinks data
... There was a bug in GDC API. They are making changes and the data was removed. They fixed and the metadata should be correct. ...
written 7 months ago by Tiago Chedraoui Silva240
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Comment: C: Missing clinical data at TCGAbiolinks data
... The API is not returning days to death anymore. And it seems it has been removed from some documentations (https://gdc.cancer.gov/clinical-data-elements), but they add year of death. I sent an email to GDC to check, but for the moment the function will not work without that information. Thanks fo ...
written 7 months ago by Tiago Chedraoui Silva240
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Comment: C: Error via running GDCdownload() in TCGAbiolinks
... The package is trying to create a file that has 267 characters (considering the full path) which more than the limit of 260 characters. You should either enable long paths ( https://www.howtogeek.com/266621/how-to-make-windows-10-accept-file-paths-over-260-characters/), or reduce the name of same fo ...
written 8 months ago by Tiago Chedraoui Silva240
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Answer: A: Error via running GDCdownload() in TCGAbiolinks
... Hello, I ran a small example and it worked. Probably the folder was not created in the system. If it is a windows OS, there is a limit of characters in the full path (I believe it is 256 characters), you might be able to check the path length it is trying to create with: stringr::strlength(file.pa ...
written 8 months ago by Tiago Chedraoui Silva240

Latest awards to Tiago Chedraoui Silva

Scholar 4 months ago, created an answer that has been accepted. For A: Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Scholar 11 months ago, created an answer that has been accepted. For A: Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Scholar 17 months ago, created an answer that has been accepted. For A: Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Scholar 2.7 years ago, created an answer that has been accepted. For A: Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Scholar 3.6 years ago, created an answer that has been accepted. For A: Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Scholar 3.6 years ago, created an answer that has been accepted. For A: Getting a flat metadata table from the XML files in TCGA: is it feasible?
Scholar 3.6 years ago, created an answer that has been accepted. For A: Multiple problems with TCGAbiolinks 2.2.6

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