User: tiagochst

gravatar for tiagochst
tiagochst60
Reputation:
60
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Trusted
Location:
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Last seen:
2 days ago
Joined:
1 year, 6 months ago
Email:
t********@usp.br

Posts by tiagochst

<prev • 37 results • page 1 of 4 • next >
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Answer: A: Problem with using GDC_queryMaf()
... Hi, GDC updated the MAF files available and there path. As the version of the package is old,  you will need to update TCGAbiolinks. The new documentation can be found at: https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/mutation.html Best regards, Tiago ...
written 6 days ago by tiagochst60
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Answer: A: Meaning of subtype_methylation.Clusters , subtype_miRNA.Clusters, subtype_CN.Clu
... Hi, Every Field with the prefix subtype came from a marker TCGA paper. You can find the list of papers on the vignette. The meaning of each column should be described in the article. Best regards, Tiago Em 2 de fev de 2017 4:45 PM, "vera [bioc]" <noreply@bioconductor.org> escreveu: > Ac ...
written 7 weeks ago by tiagochst60
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Comment: C: Getting a flat metadata table from the XML files in TCGA: is it feasible?
... Thanks, TCGA-LAML apparently does not have all the clinical information in the XML. I rewrote the code to improve it and also handle if there is a problem in the connection to GDC. ...
written 3 months ago by tiagochst60
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Answer: A: Multiple problems with TCGAbiolinks 2.2.6
... Hi,  1) By default, TCGAanalyze_survival will produce a pdf called survival.pdf.  And "Scale for 'colour'..." is just a warning. I just removed it the package, and I added a message to say that the file was created.   2) The second code does not works because we use another column (days_to_last_ ...
written 3 months ago by tiagochst60
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Answer: A: Data type error
... Hi, there is no Solid Tissue Normal samples for your search. I just fixed the error message. Best regards, Tiago ...
written 3 months ago by tiagochst60
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Comment: C: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... This function was not exported. You will need to use three ":" cnv <- TCGAbiolinks:::getGistic("HNSC") The reason it is not exported is that it downloads from gdac firehose ( http://gdac.broadinstitute.org/) and it is aligned to hg19. I'm still waiting to see if GDC will provide level 4 data f ...
written 4 months ago by tiagochst60
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Comment: C: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... Hi, I believe the package version you have is old, that table print was removed some weeks ago. Could you update it please?  Best regards, Tiago ...
written 4 months ago by tiagochst60
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Comment: C: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... Which TCGAbiolinks version do you have installed? We had a problem a month ago in this part of the code. I'm just wondering if it is the old version. ...
written 4 months ago by tiagochst60
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Answer: A: GDCPrepare function returns a function
... There was I bug. Thanks for reporting. I just solved it and it should be in bioconductor in two days. ...
written 4 months ago by tiagochst60
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Comment: C: GDCPrepare function returns a function
... Could you send your code with the query please? So I can see what is happening? ...
written 4 months ago by tiagochst60

Latest awards to tiagochst

Scholar 5 days 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 11 months 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 11 months ago, created an answer that has been accepted. For A: Multiple problems with TCGAbiolinks 2.2.6

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