Answers.Body: <p>There seems to be some problem with your &quot;platform specific tempdir&quot; that is used by getGEO's <code>destdir</code> parameter. See <code>?getGEO</code> for more info on the <code>destdir</code> parameter.</p>
  <p>Try</p>
  <pre><code>GSE68808 &lt;- getGEO(&quot;GSE68808&quot;, destdir = getwd())
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-04-06T16:33:19.293Z
Answers.LastActivityDate: 2021-04-06T16:33:19.293Z
Answers.UserDisplayName: Ram RS
Body: <p>I've installed GEOquery with</p>
  <pre class="lang-r prettyprint-override"><code>install.packages(&quot;BiocManager&quot;)
  BiocManager::install(&quot;GEOquery&quot;)
  library(GEOquery)
  </code></pre>
  <p>then I ran the command</p>
  <pre class="lang-r prettyprint-override"><code>GSE68808 &lt;- getGEO(&quot;GSE68808&quot;)
  </code></pre>
  <p>but it resulted in..</p>
  <pre class="lang-r prettyprint-override"><code>Found 1 file(s)
  GSE68808_series_matrix.txt.gz
  trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68808/matrix/GSE68808_series_matrix.txt.gz'
  Content type 'application/x-gzip' length 4138819 bytes (3.9 MB)
  downloaded 3.9 MB
  
  error: 'C:\Users\(myname)\AppData\Local\Temp\RtmpUp5Sv7\file8e844a7a59bc' does not exist.
  </code></pre>
  <p>ㅜㅜ</p>
  <p>How can I solve this? thanks.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T20:22:32.093Z
Comments.Text: Please consider accepting the answer if it has answered your question
Comments.UserDisplayName: M__
Tags: <geoquery><gse>
Title: Error downloading GSE dataset
ThreadText: # Error downloading GSE dataset
  
  (Asked by: username_0 on 2021-04-06)
  
  I've installed GEOquery with
  
  ```r
  install.packages("BiocManager")
  BiocManager::install("GEOquery")
  library(GEOquery)
  
  ```
  
  then I ran the command
  
  ```r
  GSE68808 <- getGEO("GSE68808")
  
  ```
  
  but it resulted in..
  
  ```r
  Found 1 file(s)
  GSE68808_series_matrix.txt.gz
  trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68808/matrix/GSE68808_series_matrix.txt.gz'
  Content type 'application/x-gzip' length 4138819 bytes (3.9 MB)
  downloaded 3.9 MB
  
  error: 'C:\Users\(myname)\AppData\Local\Temp\RtmpUp5Sv7\file8e844a7a59bc' does not exist.
  
  ```
  
  ㅜㅜ
  
  How can I solve this? thanks.
  
  **Tags:** geoquery, gse
  
  > **Comments:**
  > **username_1**: Please consider accepting the answer if it has answered your question  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-04-06. Score: 0
  
  There seems to be some problem with your "platform specific tempdir" that is used by getGEO's `destdir` parameter. See `?getGEO` for more info on the `destdir` parameter.
  
  Try
  
  ```
  GSE68808 <- getGEO("GSE68808", destdir = getwd())
  
  ```
  
  
  ---
  
  