Answers.Body: <p>I am not sure how appropriate it is, but GTEx data was used as the normal controls for TCGA data in <a href="https://doi.org/10.1038/s41467-017-01027-z" rel="nofollow noreferrer">Comprehensive analysis of normal adjacent to tumor transcriptomes</a>. It was not just a single panel, but a major part of the paper.</p>
  
  <p>Alternatively, there is <a href="https://github.com/mskcc/RNAseqDB" rel="nofollow noreferrer">RNAseqDB</a>:</p>
  
  <blockquote>
    <p>Here, we developped a pipeline that processes and unifies RNA-seq data
    from different studies. Using the pipeline, we have processed data
    from the GTEx and TCGA and have successfully corrected for
    study-specific biases, allowing comparative analysis across studies.</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-29T13:28:35.873Z
Answers.Text: One thing with RNAseqDB is that they provide ComBat normalized FPKM values, which cannot be used for DGE analysis with methods which require raw counts, such as DESeq2 and similar.
Answers.UserDisplayName: sus_mlm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-21T21:46:45.163Z
Answers.LastActivityDate: 2019-05-21T21:46:45.163Z
Answers.UserDisplayName: burger
Answers.Body: <p>Definately not directly. Probably not even if used indirectly. Different projects, done at different times, with different protocols, different machines, different library preps etc. </p>
  
  <p>We have tested combining GTEx and TCGA data for several different purposes where one might expect the analyses' internal controls would have allowed compatibilty, but even then we have always found a persistent batch effect which we were unable to remove. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-21T16:16:17.403Z
Answers.LastActivityDate: 2019-05-21T16:16:17.403Z
Answers.UserDisplayName: Ian Sudbery
Body: <p>I am using Recount2 TCGA data and was wondering is it right to use GTEx data as control data for this. I would really appreciate your views on this?</p>
  
Tags: <rna-seq><ngs><cancer>
Title: Can we use GTEx data as control data for TCGA data?
ThreadText: # Can we use GTEx data as control data for TCGA data?
  
  (Asked by: username_0 on 2019-05-15)
  
  I am using Recount2 TCGA data and was wondering is it right to use GTEx data as control data for this. I would really appreciate your views on this?
  
  **Tags:** rna-seq, ngs, cancer
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2019-05-21. Score: 1
  
  I am not sure how appropriate it is, but GTEx data was used as the normal controls for TCGA data in [Comprehensive analysis of normal adjacent to tumor transcriptomes](https://doi.org/10.1038/s41467-017-01027-z). It was not just a single panel, but a major part of the paper.
  
  Alternatively, there is [RNAseqDB](https://github.com/mskcc/RNAseqDB):
  
  > Here, we developped a pipeline that processes and unifies RNA-seq data
  > from different studies. Using the pipeline, we have processed data
  > from the GTEx and TCGA and have successfully corrected for
  > study-specific biases, allowing comparative analysis across studies.
  
  > **Comments:**
  > **username_2**: One thing with RNAseqDB is that they provide ComBat normalized FPKM values, which cannot be used for DGE analysis with methods which require raw counts, such as DESeq2 and similar.  
  
  ---
  
  ### Answer by username_3 on 2019-05-21. Score: 1
  
  Definately not directly. Probably not even if used indirectly. Different projects, done at different times, with different protocols, different machines, different library preps etc.
  
  We have tested combining GTEx and TCGA data for several different purposes where one might expect the analyses' internal controls would have allowed compatibilty, but even then we have always found a persistent batch effect which we were unable to remove.
  
  
  ---
  
  