Tag: tcga-brca

Index of /runs/gdc/report_2018_02_16

Name Last modified Size Description Parent Directory   –   TCGA-ACC.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 250K   TCGA-ACC.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 73K   TCGA-ACC.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 37K   TCGA-ACC.2018_02_16.sample_counts.tsv 2018-02-16 01:06 142   TCGA-BLCA.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 1.2M   TCGA-BLCA.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 90K   TCGA-BLCA.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 53K   TCGA-BLCA.2018_02_16.sample_counts.tsv 2018-02-16 01:06 201  …

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Overall survival and Event free survival

Overall survival and Event free survival 0 Hello everyone. I have a simple question. How do I calculate the overall survival (OS) rate and Event-free survival (EFS) using TCGA-BRCA clinical data? which column must be used for each one? Also, can I use the first quartile as my risk score…

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Differential expression analysis of TCGA data based on tumor staging

Hi everyone I wanted to analyze TCGA-BRCA data for identifying DEGs in different TNM stages (I to IV) between Normal and Tumor. How to change the following code to get the DEGs based on the staging? CancerProject <- “TCGA-BRCA” DataDirectory <- paste0(“../GDC/”,gsub(“-“,”_”,CancerProject)) FileNameData <- paste0(DataDirectory, “_”,”HTSeq_Counts”,”.rda”) query <- GDCquery(project =…

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Survival Analysis Cut-off

Survival Analysis Cut-off 0 Hello guys, I am doing a survival analysis using TCGA-BRCA project data. I am trying different cut-offs to separate my samples into high and low risk groups, but since it is my first time I would like to ask a question just to be fully sure…

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