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:
2 days, 2 hours ago
Joined:
3 years, 9 months ago
Email:
t********@usp.br

Posts by Tiago Chedraoui Silva

<prev • 82 results • page 1 of 9 • next >
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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 2 days 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 2 days 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 3 days 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 13 days 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 12 weeks 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 3 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 4 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 4 months ago by Tiago Chedraoui Silva240
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Comment: C: GDCdownload does not work
... You should consider the full path, not the relative path. z <- file.path(getwd(),"GDCdata/TCGA-GBM/legacy/DNA_methylation/Methylation_beta_value/0faddb5f-fe60-4269-90cd-736048a5b061/jhu-usc.edu_GBM.HumanMethylation450.6.lvl-3.TCGA-76-4926-01B-01D-1481-05.txt") length(strsplit(z, "")[[1]]) ...
written 7 months ago by Tiago Chedraoui Silva240
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Answer: A: GDCdownload does not work
... In the Windows API (with some exceptions discussed in the following paragraphs), the maximum length for a path is MAX_PATH, which is defined as 260 character (https://docs.microsoft.com/en-us/windows/desktop/fileio/naming-a-file#maximum-path-length-limitation)   In windows 10 you can enable long p ...
written 7 months ago by Tiago Chedraoui Silva240

Latest awards to Tiago Chedraoui Silva

Scholar 7 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 13 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 2.3 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 3.3 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 3.3 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 3.3 years ago, created an answer that has been accepted. For A: Multiple problems with TCGAbiolinks 2.2.6

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