User: tiagochst

gravatar for tiagochst
tiagochst100
Reputation:
100
Status:
Trusted
Location:
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Last seen:
1 day, 15 hours ago
Joined:
2 years, 2 months ago
Email:
t********@usp.br

Posts by tiagochst

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Comment: C: biomaRt: error using useDataset or useMart
... Please, was the code  updated in both Bioconductor release and devel ? ...
written 1 day ago by tiagochst100
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Comment: C: Error when prepare the TCGAdata
... I'm not sure we will be able to handle all the DNA methylation data with only 4GB. Probably the step in the code that tries to merge the objects will give you the same problem. ...
written 9 days ago by tiagochst100
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Comment: C: Error when prepare the TCGAdata
... How much memory (RAM) do you have. The problem as Marcel pointed out is that R was not able to read the data to memory. You would have to read in chunks then try to bind the objects. Something like: #Load Package library("TCGAbiolinks") #TCGA query LUAD.met<-GDCquery(project = "TCGA-LUAD", ...
written 11 days ago by tiagochst100
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Comment: C: Cannot retrieve projects from TCGA using getGDCprojects function
... Please, which version of the package are you using? I don't get that with the last version. Could you please update it from the github: devtools::install_github('BioinformaticsFMRP/TCGAbiolinks') ...
written 18 days ago by tiagochst100
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Comment: C: update TCGAbiolinks to version 3.6 and GDCquery doesn't work
... Hi, I just update the release version with the fixes from devel. It should be working in a couple of days. For the moment could you use the github version? You can install it with devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks") ...
written 5 weeks ago by tiagochst100
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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 8 months ago by tiagochst100
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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 8 months ago by tiagochst100
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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 8 months ago by tiagochst100
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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 8 months ago by tiagochst100
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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 8 months ago by tiagochst100

Latest awards to tiagochst

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 20 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 20 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 20 months ago, created an answer that has been accepted. For A: Multiple problems with TCGAbiolinks 2.2.6

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