User: tiagochst

gravatar for tiagochst
tiagochst70
Reputation:
70
Status:
Trusted
Location:
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Last seen:
4 months ago
Joined:
1 year, 11 months ago
Email:
t********@usp.br

Posts by tiagochst

<prev • 45 results • page 1 of 5 • next >
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... I also got this bug when I used biomart version < 2.31.10. The 2.31.10 seems to be working correctly. Could you check your biomart version, please? ...
written 4 months ago by tiagochst70
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... And does install.packages("psych") work? ...
written 4 months ago by tiagochst70
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... Please, could you check if your TCGAbiolinks version is equal to 2.3.22 and biomart to 2.31.10? The output you have is not the last version. ...
written 4 months ago by tiagochst70
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... Please, did you propagate this function to release or it will be only in the devel? ...
written 4 months ago by tiagochst70
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
...   Version 2.31.9 gave me this: > useEnsembl("ensembl",  +            dataset = "hsapiens_gene_ensembl",  +            mirror = "uswest") Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  :    Unexpected format to the list of available marts. Please check the follow ...
written 4 months ago by tiagochst70
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... I commited the fix yesterday. https://github.com/BioinformaticsFMRP/TCGAbiolinks/commit/39265220f7cfeb677c3133f13214ffc4abf6df91   It was working with the last development version of biomaRt (2.31.7). You can install it with devtools::install_github("Bioconductor-mirror/biomaRt") devtools::ins ...
written 4 months ago by tiagochst70
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... We use biomaRt to download the last version of the genome. I have the same error using the following code:  biomaRt::listMarts(host="www.ensembl.org") ...
written 4 months ago by tiagochst70
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Answer: A: Extract gene expression values from GDCprepare object
... Hi, The default GDCprepare output is a SummarizedExperiment (SE) object, but you can also set to output the data frame. The main difference is the the SE  has gene information (start, end and others) and sample information. https://gist.github.com/tiagochst/8c4bccea3bb0f2b022b7c22c73b0e9dc There ...
written 4 months ago by tiagochst70
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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 5 months ago by tiagochst70
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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 6 months ago by tiagochst70

Latest awards to tiagochst

Scholar 5 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 16 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 16 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 16 months ago, created an answer that has been accepted. For A: Multiple problems with TCGAbiolinks 2.2.6

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