Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-19T17:25:15.647Z
Answers.Text: I've added an image of the UCI dataset. I just need to perform a query that returns similar kind of gene expression level tabular data. 
  
  As the query only returns TCGA-BRCA data only, will replicating the query for other four types create similar (biologically equivalent and meaningful) kind of dataset?
Answers.UserDisplayName: fuad021
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-19T18:07:55.593Z
Answers.Text: Yes, you can change the cancer type and re-use the query but my main concern is the type of data that this query would return. Your query fetches count data via the `HTSeq - Counts` filter but in the posted image, there are floats instead of integers (gene counts), this can be normalized data. If I remember correctly, HTSeq-Counts should be returning actual counts, so integers.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-19T08:02:45.877Z
Answers.LastActivityDate: 2022-02-19T08:02:45.877Z
Answers.UserDisplayName: haci
Body: <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.sstatic.net/oy67i.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/7zPXN.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-18T16:57:22.100Z
Comments.Text: Not quite what I was hoping for the query rather than the raw link ... Anyway I guess I wasn't clear
Comments.UserDisplayName: M__
Tags: <genome><database><gene-expression><cancer>
Title: Querying The Cancer Genome Atlas (TCGA) for gene expression
ThreadText: # Querying The Cancer Genome Atlas (TCGA) for gene expression
  
  (Asked by: username_0 on 2022-02-18)
  
  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:
  
  [![gene expression UCI dataset](https://i.sstatic.net/oy67i.png)](https://i.sstatic.net/oy67i.png)
  
  How to query in The Cancer Genome Atlas (TCGA) to create an updated version of this dataset?
  
  I've done the following [query](https://portal.gdc.cancer.gov/&searchTableTab=files).
  
  [![same query in visual form](https://i.sstatic.net/7zPXN.png)](https://i.sstatic.net/7zPXN.png)
  
  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.
  
  **Tags:** genome, database, gene-expression, cancer
  
  > **Comments:**
  > **username_1**: Not quite what I was hoping for the query rather than the raw link ... Anyway I guess I wasn't clear  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-02-19. Score: 2 | Accepted answer
  
  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](https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html), 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/>
  
  > **Comments:**
  > **username_0**: I've added an image of the UCI dataset. I just need to perform a query that returns similar kind of gene expression level tabular data.   As the query only returns TCGA-BRCA data only, will replicating the query for other four types create similar (biologically equivalent and meaningful) kind of dataset?  
  > **username_2**: Yes, you can change the cancer type and re-use the query but my main concern is the type of data that this query would return. Your query fetches count data via the `HTSeq - Counts` filter but in the posted image, there are floats instead of integers (gene counts), this can be normalized data. If I remember correctly, HTSeq-Counts should be returning actual counts, so integers.  
  
  ---
  
  