User: Tiago Chedraoui Silva

Reputation:
170
Status:
Trusted
Location:
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Scholar ID:
Google Scholar Page
Last seen:
3 months ago
Joined:
3 years, 5 months ago
Email:
t********@usp.br

Posts by Tiago Chedraoui Silva

<prev • 76 results • page 1 of 8 • next >
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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 16 days ago by Tiago Chedraoui Silva170
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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 16 days ago by Tiago Chedraoui Silva170
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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 3 months ago by Tiago Chedraoui Silva170
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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 3 months ago by Tiago Chedraoui Silva170
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Comment: C: Duplicate issue in ELMER get.pair for HNSC data
... There was some genes that had different entrezid for the same emsembleID. I commit a fix to consider that case.  Please, could you reinstall from github with: devtools::install_github("tiagochst/ELMER") ...
written 4 months ago by Tiago Chedraoui Silva170
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Comment: C: Duplicate issue in ELMER get.pair for HNSC data
... Please, which ELMER version is installed ?  ...
written 4 months ago by Tiago Chedraoui Silva170
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Comment: C: Error in print.header("GDCquery: Searching in GDC database", "section") :could n
... Hi, this is an internal function, but it should be visible. Please, could you sent the listSamples and the package version (packageVersion("TCGAbiolinks"))? ​       ...
written 6 months ago by Tiago Chedraoui Silva170
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Comment: C: TCGAbiolinksGUI is not stable on windows 7.
... We added a function to normalized DNA methylation idats that uses that missing package (although we might change to sesame in the future). You should be able to install the missing dependency with: source("https://bioconductor.org/biocLite.R") biocLite("IlluminaHumanMethylationEPICanno.ilm10b2.hg1 ...
written 6 months ago by Tiago Chedraoui Silva170
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Comment: C: TCGAbiolinksGUI is not stable on windows 7.
... Please, could you try the GitHub version? You can install with: ​devtools::install_github("BioinformaticsFMRP/TCGAbiolinksGUI") ...
written 6 months ago by Tiago Chedraoui Silva170
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Comment: C: TCGA biolinks - Samples with multiple profiles
... The way TCGAbiolinks was structured it is not possible to do the query requested. You would need to go through a series of single manifests, filtering and merging.I'm not sure which WXS data you wanted, or which RNA-seq but the code below can be easily modified. https://gist.github.com/tiagochst/83 ...
written 6 months ago by Tiago Chedraoui Silva170

Latest awards to Tiago Chedraoui Silva

Scholar 9 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 2.0 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 2.9 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 2.9 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 2.9 years ago, created an answer that has been accepted. For A: Multiple problems with TCGAbiolinks 2.2.6

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