Answers.Body: <p>If it's not in there then you can either email the authors or just live with it. It is fully on the authors what you upload to NCBI. Nobody at NCBI checks the actual content of the uploads in terms of whether it indeed contains what methods texts or the paper pretend that it contains. Nor do (usually) the reviewers. Published data are great in terms of having a large repository of resources and knowledge available, downside is that metadata are often a mess or absent. There is no general and easy answer to this.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-03-19T09:35:12.037Z
Answers.LastActivityDate: 2024-03-19T09:35:12.037Z
Answers.UserDisplayName: ATpoint
Body: <p>When downloading GSE data, often I encounter that the authors refer to additional visits in the data description, yet, they are not found in the data.</p>
  <p>For example, the following <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72326" rel="nofollow noreferrer">study</a>. They mention additional visits, however inspecting the phenotype data extracted using <code>getGEO</code> function does not show them (only baseline). The same happens with different studies as well, for example this <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE88885" rel="nofollow noreferrer">study</a>.</p>
  <p>Example to how I extract the phenotype data:</p>
  <pre><code>gsm &lt;- getGEO('GSE88885', GSEMatrix = TRUE)
  gsm &lt;- gsm[[1]]
  pheno_dat &lt;- gsm@phenoData@data %&gt;% as.data.frame() 
  </code></pre>
  <p>Am I missing some additional data?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-19T11:05:55.857Z
Comments.Text: Can you please explain what you mean by "visits"?
Comments.UserDisplayName: gringer
Tags: <rna-seq><differential-expression><public-databases><geoquery><gse>
Title: missing additional visits in GSE data
ThreadText: # missing additional visits in GSE data
  
  (Asked by: username_0 on 2024-03-19)
  
  When downloading GSE data, often I encounter that the authors refer to additional visits in the data description, yet, they are not found in the data.
  
  For example, the following [study](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72326). They mention additional visits, however inspecting the phenotype data extracted using `getGEO` function does not show them (only baseline). The same happens with different studies as well, for example this [study](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE88885).
  
  Example to how I extract the phenotype data:
  
  ```
  gsm <- getGEO('GSE88885', GSEMatrix = TRUE)
  gsm <- gsm[[1]]
  pheno_dat <- gsm@phenoData@data %>% as.data.frame() 
  
  ```
  
  Am I missing some additional data?
  
  **Tags:** rna-seq, differential-expression, public-databases, geoquery, gse
  
  > **Comments:**
  > **username_1**: Can you please explain what you mean by "visits"?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-03-19. Score: 1
  
  If it's not in there then you can either email the authors or just live with it. It is fully on the authors what you upload to NCBI. Nobody at NCBI checks the actual content of the uploads in terms of whether it indeed contains what methods texts or the paper pretend that it contains. Nor do (usually) the reviewers. Published data are great in terms of having a large repository of resources and knowledge available, downside is that metadata are often a mess or absent. There is no general and easy answer to this.
  
  
  ---
  
  