User: tiagochst

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tiagochst130
Reputation:
130
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Trusted
Location:
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Last seen:
4 weeks ago
Joined:
2 years, 9 months ago
Email:
t********@usp.br

Posts by tiagochst

<prev • 65 results • page 1 of 7 • next >
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Answer: C: TCGAbiolinks gives error when parsing a txt file (instead of expected xml)
... Hello I fixed the documentation yesterday. It seems the parsed TXT were added to the same group as the XML files. You need to add file.type = "xml" as filter.  query <- GDCquery(project = 'TCGA-KIRC', data.category = "Clinical",file.type = "xml") ...
written 4 weeks ago by tiagochst130
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Comment: C: GDCquery fail in some project , for example: TCGA-COAD mRNA
... GDC api moved to another path. Some versions of libcurl seems not to be able to redirect. We updated the link to api. It should be fixed now. Could you please update the package from github with devtools::install_github("BioinformaticsFMRP/TCGAbiolinks") Best regards, Tiago ...
written 6 weeks ago by tiagochst130
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Comment: C: GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-REA
... Hello,   I just made an update I believe will solve the problem. Could you update the package from github with devtools::install_github("BioinformaticsFMRP/TCGAbiolinks") and test it, please? ...
written 6 weeks ago by tiagochst130
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Comment: C: DESeq2 differential analysis - log2FC doubt
... Thank you very much for the help! ...
written 7 weeks ago by tiagochst130
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Comment: C: DESeq2 differential analysis - log2FC doubt
... But that's weird because I did not get that. And the rownames and colnames were different.   > colnames(all_cell_lines_ordered[,-c(1:7)],) [1] "IOSE11" "IOSE4" "FT246" "FT33" "EEC16" "EFO27" "GTFR230" "MCAS" "OAW42" "VOA1056" "CaOV3" "HEY" "UWB1_ ...
written 7 weeks ago by tiagochst130
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Comment: C: DESeq2 differential analysis - log2FC doubt
... Thanks! I thought it was going to do the same thing Summarized Experiment does, it checks if rownames and colnames match (even though my code was not going to work since rownames were empty) ...
written 7 weeks ago by tiagochst130
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Comment: C: DESeq2 differential analysis - log2FC doubt
... I added the data here: https://drive.google.com/drive/folders/1p5CDMR2OOMCbT2WXRNtNRUrv4f3FhCNo?usp=sharing ...
written 7 weeks ago by tiagochst130
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Comment: C: DESeq2 differential analysis - log2FC doubt
... Yes, the meatada in dds has different labels (JHOC5 was in group E in Metadata_table, but in dds it is labeled as C) http://rpubs.com/tiagochst/392569 ...
written 7 weeks ago by tiagochst130
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Comment: C: DESeq2 differential analysis - log2FC doubt
... So the plot is correlated with results. But is it possible that a 0 count for all samples in a group increase if normalized ? It seems the number of samples in each group are correct. http://rpubs.com/tiagochst/392569 ...
written 7 weeks ago by tiagochst130
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Comment: C: DESeq2 differential analysis - log2FC doubt
... Yes. But: - DEA section, second chunk, third line. I use E as reference  - DEA section, forth chunk, first line. I use A as reference But E is more expressed than A for gene ST13P12 (section Gene ST13P12, avg.count), and setting E as reference gives me log2FC > 0. It should be the opposite no ...
written 7 weeks ago by tiagochst130

Latest awards to tiagochst

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

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