text: user15079: The UCI gene expression cancer RNA-Seq ​dataset (https://archive.ics.uci.edu/ml/datasets/gene+expression+cancer+RNA-Seq) consists of 5 types of cancers (BRCA, KIRC, LUAD, COAD, PRAD) and gene expression levels of 20,531 genes for 801 samples. The dataset looks like this:
  
  How to query in The Cancer Genome Atlas (TCGA) to create an updated version of this dataset?
  I've done the following query.
  
  Is the given query and the UCI dataset equivalent? If not, how to query properly?
  P.S.: I'm a CS student; do not have any biology background.
  
  user3541: To start with, your query above is selecting for breast cancer samples (TCGA-BRCA) only. The original dataset seems to contain 4 other cancer types.
  The link you provided has a link to https://www.synapse.org/#!Synapse:syn4301332 and by looking at filenames of the 14 files there, I can tell that there are different types of data: miRNA expression, gene expression, methylation, ... And your query is limited to gene expression only. I am not even sure if you can use just a single query to fetch all of the 14 data files, you might need to use multiple queries.
  If you are familiar with R, I would recommend TCGABiolinks, it will abstract away a lot of otherwise annoying manual steps. Apparently you can also use Python retrieve TCGA data:https://docs.gdc.cancer.gov/API/Users_Guide/Python_Examples/
  
original_text: 15079: <p>The UCI gene expression cancer RNA-Seq ​dataset (<a href="https://archive.ics.uci.edu/ml/datasets/gene+expression+cancer+RNA-Seq" rel="nofollow noreferrer">https://archive.ics.uci.edu/ml/datasets/gene+expression+cancer+RNA-Seq</a>) consists of 5 types of cancers (BRCA, KIRC, LUAD, COAD, PRAD) and gene expression levels of 20,531 genes for 801 samples. The dataset looks like this:</p>
  <p><a href="https://i.stack.imgur.com/oy67i.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/oy67i.png" alt="gene expression UCI dataset" /></a></p>
  <p>How to query in The Cancer Genome Atlas (TCGA) to create an updated version of this dataset?</p>
  <p>I've done the following <a href="https://portal.gdc.cancer.gov/&amp;searchTableTab=files" rel="nofollow noreferrer">query</a>.</p>
  <p><a href="https://i.stack.imgur.com/7zPXN.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/7zPXN.png" alt="same query in visual form" /></a></p>
  <p>Is the given query and the UCI dataset equivalent? If not, how to query properly?</p>
  <p>P.S.: I'm a CS student; do not have any biology background.</p>
   3541: <p>To start with, your query above is selecting for breast cancer samples (TCGA-BRCA) only. The original dataset seems to contain 4 other cancer types.</p>
  <p>The link you provided has a link to <a href="https://www.synapse.org/#!Synapse:syn4301332" rel="nofollow noreferrer">https://www.synapse.org/#!Synapse:syn4301332</a> and by looking at filenames of the 14 files there, I can tell that there are different types of data: miRNA expression, gene expression, methylation, ... And your query is limited to gene expression only. I am not even sure if you can use just a single query to fetch all of the 14 data files, you might need to use multiple queries.</p>
  <p>If you are familiar with R, I would recommend <a href="https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html" rel="nofollow noreferrer">TCGABiolinks</a>, it will abstract away a lot of otherwise annoying manual steps. Apparently you can also use Python retrieve TCGA data:<a href="https://docs.gdc.cancer.gov/API/Users_Guide/Python_Examples/" rel="nofollow noreferrer">https://docs.gdc.cancer.gov/API/Users_Guide/Python_Examples/</a></p>
  